Relocate wiki from trac

rewritten to use Path.contains_points.

LICENSE

@@ -276,64 +276,3 @@ TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
 YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
 PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGES.
-
-		     END OF TERMS AND CONDITIONS
-
-	    How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-
-    Gnomovision version 69, Copyright (C) year name of author
-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary.  Here is a sample; alter the names:
-
-  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-  `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
-  <signature of Ty Coon>, 1 April 1989
-  Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs.  If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.

Makefile.m4

@@ -0,0 +1,30 @@
+PREFIX=M4_PREFIX
+BIN_DIR=M4_BINDIR
+DATA_DIR=M4_DATADIR
+PY_DIR=M4_PYDIR
+DOC_DIR=M4_DOCDIR
+
+SCRIPTS_DIR=${DATA_DIR}/laydi/scripts/
+
+install: install_laydi install_doc
+
+install_laydi:
+	## Install binary files		
+	install -m 755 -D bin/laydi ${BIN_DIR}/laydi
+	install -m 755 -D bin/dataset ${BIN_DIR}/dataset
+	
+	## Install library files
+	find laydi/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \;
+	find laydi/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \;
+	
+	## Install icons
+	find icons/ -type f -name '*.png' -exec install -m 644 -D {} ${DATA_DIR}/{} \;
+
+install_scripts:
+	find scripts/ -type f -exec install -D {} ${SCRIPTS_DIR}/{} \;
+
+install_doc:
+	DOC_DIR=${DOC_DIR}/ make -C doc install
+	install -m 644 README ${DOC_DIR}/
+	install -m 644 LICENSE ${DOC_DIR}/
+

R/laydi/DESCRIPTION

@@ -0,0 +1,10 @@
+Package: laydi
+Type: Package
+Title: Interface to Laydi
+Version: 0.1.0
+Date: 2011-03-05
+Author: Einar Ryeng <einarr@pvv.ntnu.no>
+Maintainer: Einar Ryeng <einarr@pvv.ntnu.no>
+Description: R interface to Laydi
+License: LGPL
+LazyLoad: yes

R/laydi/R/laydi.R

@@ -0,0 +1,61 @@
+
+write.ftsv <- function(data, con, name="unnamed_dataset", rowdim="rows", coldim="cols") {
+    # If con is a file name, open it 
+    opened.here = FALSE
+    if (is.character(con)){
+        con = file(con, "w")
+        opened.here = TRUE 
+    }
+    
+    # Substitute all whitespace with underscores in identifiers 
+    rows <- paste(gsub("\\s", "_", rownames(data)), collapse=" ")
+    cols <- paste(gsub("\\s", "_", colnames(data)), collapse=" ")
+
+    # Write header 
+    writeLines(c("# type: dataset", 
+                 paste("# dimension:", rowdim, rows, collapse=' '), 
+                 paste("# dimension:", coldim, cols, collapse=' '), 
+                 paste("# name:", name, collapse=' '),
+                 ""),
+               con=con)
+
+    # Write matrix 
+    write.table(data, file=con, col.names=FALSE, row.names=FALSE, sep="\t")
+
+    # If con was a string, close file now 
+    if (opened.here)
+        close(con)
+}
+
+write.laydi.selection <- function(data, con) {
+    # If con is a file name, open it 
+    opened.here = FALSE
+    if (is.character(con)){
+        con = file(con, "w")
+        opened.here = TRUE 
+    }
+    
+    writeLines(gsub("\\s", "_", data), con=con)
+    
+    # If con was a string, close file now 
+    if (opened.here)
+        close(con)
+}
+
+read.laydi.selection <- function(con) {
+    # If con is a file name, open it 
+    opened.here = FALSE
+    if (is.character(con)){
+        con = file(con)
+        opened.here = TRUE 
+    }
+    
+    ids <- readLines(con=con, encoding="UTF-8")
+    
+    # If con was a string, close file now 
+    if (opened.here)
+        close(con)
+
+    ids
+}
+

R/laydi/man/laydi-package.Rd

@@ -0,0 +1,38 @@
+\name{laydi-package}
+\alias{laydi-package}
+\alias{laydi}
+\docType{package}
+\title{Interface to Laydi}
+\description{
+Interface to Laydi files and projects. Allows writing R matrices to laydi data files.
+}
+\details{
+\tabular{ll}{
+Package: \tab laydi\cr
+Type: \tab Package\cr
+Version: \tab 0.1.0\cr
+Date: \tab 2011-03-05\cr
+License: \tab LGPL\cr
+LazyLoad: \tab yes\cr
+}
+
+library(laydi)
+write.ftsv(matrix, file, ...)
+write.laydi.selection(idlist, file)
+
+}
+\author{
+Einar Ryeng <einarr@pvv.org>\cr
+Arnar Flatberg <arnar.flatberg@gmail.com>
+
+Maintainer: Einar Ryeng <einarr@pvv.org>
+}
+\references{
+}
+\keyword{ package }
+\seealso{
+% ~~ Optional links to other man pages, e.g. ~~
+% ~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+}
+\examples{
+}

R/laydi/man/read.laydi.selection.Rd

@@ -0,0 +1,53 @@
+\name{read.laydi.selection}
+\alias{read.laydi.selection}
+\title{read.laydi.selection}
+\description{
+Reads a list of identifiers from a file.
+}
+\usage{
+read.laydi.selection(con)
+}
+\arguments{
+  \item{con}{
+     Connection (or file name) to read from. If con is a character string, it
+     will be treated as a file name, and the file will be opened, read and
+     closed.  If con is an open connection (file descriptor), the file will
+     remain open.
+  }
+}
+
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+Laydi and the laydi R package are not published in the litterature. Source code
+can be found at http://dev.pvv.ntnu.no/projects/laydi
+}
+\author{
+Einar Ryeng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+
+read.laydi.selection("/tmp/selected_samples")
+
+}
+
+\keyword{ IO }
+\keyword{ file }
+

R/laydi/man/write.ftsv.Rd

@@ -0,0 +1,74 @@
+\name{write.ftsv}
+\alias{write.ftsv}
+\title{write.ftsv}
+\description{
+Writes a matrix to a ftsv (laydi dataset) file. The matrix must have rownames
+and colnames. Rownames and colnames must be unique, and whitespace characters
+will be replaced with underscores.
+}
+\usage{
+write.ftsv(data, con, name = "unnamed_dataset", rowdim = "rows", coldim = "cols")
+}
+\arguments{
+  \item{data}{
+     A data matrix. All items in rownames(data) and colnames(data) must be
+     unique, and all whitespace characters will be replaced wity underscores in
+     the output. (Laydi requires unique identifiers along a dimension, and does
+     not allow identifiers to contain spaces.)
+  }
+  \item{con}{
+     Connection (or file name) to write the data to. If con is a character
+     string, it will be treated as a file name, and a file by that name will be
+     created, written to and closed. If con is an open connection (file descriptor),
+     the file will remain open.
+  }
+  \item{name}{
+     Datasets in laydi have a name.
+  }
+  \item{rowdim}{
+     Laydi names all dimensions of matrices. rowdim is the dimension
+     name for rows in the the file. E.g. "samples", if rows denotes samples.
+  }
+  \item{coldim}{
+     Laydi names all dimensions of matrices. coldim is the dimension
+     name for columns in the the file. E.g. "gene-ids" if columns represent
+     genes.
+  }
+}
+
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+Laydi and this R package are not published in the litterature. Source code can be found at
+http://dev.pvv.ntnu.no/projects/laydi
+}
+\author{
+Einar Ryeng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+
+library(datasets)
+write.ftsv(randu, "/tmp/randu.ftsv")
+
+}
+
+\keyword{ IO }
+\keyword{ file }
+

R/laydi/man/write.laydi.selection.Rd

@@ -0,0 +1,61 @@
+\name{write.laydi.selection}
+\alias{write.laydi.selection}
+\title{write.laydi.selection}
+\description{
+Writes a Laydi selection file from a list of identifiers. Identifiers are
+written one per line, with all whitespace characters substituted with
+underscores.
+}
+\usage{
+write.laydi.selection(data, con)
+}
+\arguments{
+  \item{data}{
+     A list of identifiers. All whitespace characters will be replaced wity
+     underscores in the output. (Laydi requires unique identifiers along a
+     dimension, and does not allow identifiers to contain spaces.) This method
+     does not ensure that identifiers are unique.  
+  }
+  \item{con}{
+     Connection (or file name) to write the data to. If con is a character
+     string, it will be treated as a file name, and a file by that name will be
+     created, written to and closed. If con is an open connection (file descriptor),
+     the file will remain open.
+  }
+}
+
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+Laydi and the laydi R package are not published in the litterature. Source code
+can be found at http://dev.pvv.ntnu.no/projects/laydi
+}
+\author{
+Einar Ryeng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+
+write.laydi.selection(c("sample1", "sample2", "sample3"), "/tmp/selected_samples")
+
+}
+
+\keyword{ IO }
+\keyword{ file }
+

README

@@ -1,27 +0,0 @@
-Fluents Data Analysis Software
-
-LICENSE
--------
-Fluents is relased under the terms of the GNU GPL, included in the LICENSE file
-in this directory.
-
-DOCUMENTATION
--------------
-The primary and canonical source of documentation is the source code. If a
-keyboard shortcut is listed on the wiki but it does not work in the program,
-the program is right, and the wiki is wrong.
-
-That said, the next best place to look for documentation is the project wiki,
-located at https://dev.pvv.ntnu.no/projects/fluent/help
-
-BUILDING
---------
-Fluents is a python program, and as such, python will build compiled versions
-of each .py file as it loads them. You do not need to explicitly compile the
-program.
-
-TODO
-----
-The current TODO list can be found on
-https://dev.pvv.ntnu.no/projects/fluent/report/1 
-

README.md

@@ -0,0 +1,57 @@
+![](./wiki/graphics/project_icon.png)
+
+# Laydi
+
+## Look At Your Data Interactively
+
+Laydi is an acronym for look at your data interactively, which is what the program is aimed at. It is a lightweight data analysis program for bilinear modeling (PCA and PLS) with a strong focus on interactive use. Laydi is released under the GNU GPL and the latest development snapshot can be downloaded from https://git.pvv.ntnu.no/Projects/laydi.git
+
+![](./wiki/graphics/screenshot-00.png)
+
+## Features
+
+- Principal Component Analysis (PCA)
+- Partial Least Squares Regression (PLS)
+- L-shaped PLS regression (L-PLS)
+- Easy mapping of variables between plots, selections in one plot propagates to other plots.
+
+## Nonfeatures
+
+- Does not import arbitrary files. Files must be prepared in a (simple) file format prior to import.
+- Saving and loading of projects is not implemented. (Datasets can be saved and loaded, though, and plots can be exported)
+- Not very stable
+
+## Installation requirements
+
+Laydi currently requires the following extra packages, available from apt on Debian and Ubuntu.
+
+- python2.4 or python2.5
+- python-glade2
+- python-gnome2
+- python-gtk2
+- python-matplotlib
+- python-scipy
+- python-numpy
+
+Partially needed
+
+- python-networkx
+- python-pygraphviz
+
+## Download laydi
+
+Laydi is not debianized. To download it, use the clone the git repo.
+
+```console
+git clone https://git.pvv.ntnu.no/Projects/laydi.git
+```
+
+## User documentation
+
+- [Frequently Asked Questions](./wiki/faq.md)
+- [Laydi help](./wiki/help.md) (the same as available through the help menu in the application.)
+- [Terminology](./wiki/Terminology.md)
+
+## Developer documentation
+
+- [Developer tips and tricks](./wiki/development/hints.md)

README.old

@@ -0,0 +1,41 @@
+Laydi Data Analysis Software
+
+LICENSE
+-------
+Laydi is relased under the terms of the GNU GPL, included in the LICENSE file
+in this directory.
+
+DOCUMENTATION
+-------------
+The primary and canonical source of documentation is the source code. If a
+keyboard shortcut is listed on the wiki but it does not work in the program,
+the program is right, and the wiki is wrong.
+
+That said, the next best place to look for documentation is the project wiki,
+located at https://dev.pvv.ntnu.no/projects/laydi/help
+
+Class documentation is in HTML form in the doc/ directory.
+
+BUILDING
+--------
+Laydi is a python program, and as such, python will build compiled versions
+of each .py file as it loads them. You do not need to explicitly compile the
+program.
+
+If you have just checked out the program to a directory named laydi, e.g. with
+the command:
+
+svn co https://dev.pvv.org/svn/laydi/trunk laydi
+
+you can run it by typing:
+
+cd laydi
+./configure --prefix=`pwd`/build
+make
+./run-laydi
+
+TODO
+----
+The current TODO list can be found on
+https://dev.pvv.ntnu.no/projects/laydi/report/1 
+

bin/dataset

@@ -0,0 +1,116 @@
+#!/usr/bin/python
+
+import os,sys
+from laydi import dataset
+import cfgparse, optparse
+import re
+
+PROGRAM_NAME = 'dataset'
+VERSION = '0.1.0'
+
+def read_dataset_header(input):
+    name = ""
+    type = ""
+    dimensions = []
+
+    kv_re = re.compile('^\s*#\s*(\w+)\s*:(.*)$')
+
+    lines = []
+    line = input.readline()
+    while line.startswith('#'):
+        lines.append(line)
+        line = input.readline()
+
+    for line in lines:
+        match = kv_re.match(line)
+        if not match:
+            continue
+        k, v = match.groups()
+        k = k.strip()
+        
+        if k == 'name':
+            name = v
+        elif k == 'type':
+            type = v
+        elif k == 'dimension':
+            values = v.split()
+            dimensions.append((values[0], values[1:]))
+    
+    return (name, type, dimensions)
+
+def show_info(input):
+    name, type, dimensions = read_dataset_header(input)
+
+    print "Name: %s" % name
+    print "Type: %s" % type
+    print "Dimensions:",
+    for i, dim in enumerate(dimensions):
+        dimname = dim[0]
+        length = len(dim[1])
+        print "%s(%i)" % (dimname, length),
+        if i < len(dimensions)-1:
+            print "x",
+    print
+
+def list_dimension_ids(input, dimname):
+    name, type, dimensions = read_dataset_header(input)
+    for i, dim in enumerate(dimensions):
+        name, ids = dim
+        if name == dimname:
+            for id in ids:
+                print id
+            
+def parse_options():
+    conf_files = ['/etc/laydirc',
+                  os.path.join(os.environ['HOME'], '.laydi')]
+
+    cp = cfgparse.ConfigParser()
+    op = optparse.OptionParser()
+
+    op.add_option('-c', '--csv',
+                  action='store_true', default=False,
+                  help='Export as CSV file.')
+
+    op.add_option('-d', '--dimension',
+                  action='store', default=None,
+                  help='Get all identifiers along a dimension.')
+
+    op.add_option('-i', '--info',
+                  action='store_true', default=False,
+                  help='Show dataset information.')
+
+    op.add_option('-l', '--longinfo',
+                  action='store_true', default=False,
+                  help='Display more information than -i.')
+
+    op.add_option('-o', '--output-file',
+                  action='store_true', default=False,
+                  help='Send output to file instead of stdout.')
+
+    op.add_option('-t', '--transpose',
+                  action='store_true', default=False,
+                  help='Transpose dataset.')
+
+    op.add_option('-y', '--change-type',
+                  action='store_true', default=False,
+                  help='Set new dataset type.')
+
+
+    for cf in conf_files:
+        if os.path.isfile(cf):
+            cp.add_file(cf)
+
+    return cp.parse(op)
+
+if __name__ == '__main__':
+    options, params = parse_options()
+    input = sys.stdin
+    output = sys.stdout
+
+    if options.info:
+        show_info(input)
+        sys.exit(0)
+
+    elif options.dimension != None:
+        list_dimension_ids(input, options.dimension)
+    

bin/ftsv2csv

@@ -0,0 +1,50 @@
+#!/usr/bin/python
+
+import sys
+
+from laydi import dataset
+from getopt import getopt
+
+def read_options():
+    short_opts = ""
+    long_opts = []
+
+    options, params = getopt(sys.argv[1:], short_opts, long_opts)
+
+    return params
+
+
+def write_csv(fd, ds):
+    rowdim, coldim = ds.get_dim_name()
+    rowids = ds.get_identifiers(rowdim, sorted=True)
+    colids = ds.get_identifiers(coldim, sorted=True)
+    x = ds.asarray()
+
+    ## Print ID row
+    print >> fd, rowdim,
+    for id in colids:
+        print >> fd, id,
+    print >> fd
+    
+    ## Print column IDs and data
+    for i, row in enumerate(rowids):
+        print >> fd, row,
+        for j in range(len(colids)):
+            print >> fd, x[i,j],
+        print >> fd
+
+if __name__ == "__main__":
+    params = read_options()
+    input_fn = params[0]
+
+    if len(params) == 2:
+	output_fn = params[1]
+    else:
+        name, ext = input_fn.rsplit('.', 1)
+        output_fn = name + '.csv'
+
+    ds = dataset.read_ftsv(input_fn)
+    output_fd = open(output_fn, 'w')
+    write_csv(output_fd, ds)
+    output_fd.close()
+

bin/laydi

@@ -0,0 +1,145 @@
+#!/usr/bin/python
+
+from getopt import getopt
+import os
+import sys
+from laydi import laydi, project, projectview, workflow, main
+#import workflows
+from laydi import cfgparse
+import optparse
+
+PROGRAM_NAME = 'laydi'
+VERSION = '0.1.0'
+
+def list_workflows():
+    print 'laydi %s' % VERSION
+    print
+    print 'Available workflows:'
+
+    wfs = workflow.workflow_list()
+    for wf in wfs:
+        print '    %s (%s)' % (wf.ident, wf.name)
+    print
+
+
+def generate_config():
+    fn = os.path.join(os.environ['HOME'], '.laydi')
+    if not os.path.exists(fn):
+	fd = open(fn, 'w')
+	print >> fd, "home = %s" % os.environ['HOME']
+        print >> fd, "datadir = %%(home)s/laydi/datasets"
+        print >> fd, "workflowdir = %%(home)s/laydi/workflows"
+	fd.close()
+   
+    laydidir = os.path.join(os.environ['HOME'], 'laydi')
+    if not os.path.exists(laydidir):
+	os.mkdir(laydidir, 0755)
+
+    datadir = os.path.join(os.environ['HOME'], 'laydi/datasets')
+    if not os.path.exists(datadir):
+	os.mkdir(datadir, 0755)
+
+    workflowdir = os.path.join(os.environ['HOME'], 'laydi/workflows')
+    if not os.path.exists(workflowdir):
+	os.mkdir(workflowdir, 0755)
+
+
+def parse_options():
+    conf_files = ['/etc/laydirc',
+                  os.path.join(os.environ['HOME'], '.laydi')]
+
+    cp = cfgparse.ConfigParser()
+
+    cp.add_option('home', type='string',
+                  default=os.environ['HOME'])
+
+    cp.add_option('datadir', type='string',
+                  default=os.environ['HOME'])
+    cp.add_option('workflowdir', type='string',
+                  default='workflows')
+    cp.parse()
+    op = optparse.OptionParser()
+
+    op.add_option('-l', '--list-workflows',
+                  action='store_true',
+                  default=False,
+                  help='List available workflows.')
+
+    op.add_option('-w', '--workflow',
+                 default='default',
+                 help='Start with selected workflow')
+
+    op.add_option('-c', '--generate-config',
+                 action='store_true',
+                 help='Generate configuration file ~/.laydi if it does not exist.')
+
+    op.add_option('-n', '--new-project',
+                  action='store_true',
+                  help='Create new project directory.')
+
+    for cf in conf_files:
+        if os.path.isfile(cf):
+            cp.add_file(cf)
+
+    options, params = cp.parse(op)
+    if len(params) != 1:
+        print "error: project directory must be specified."
+        print "notice: to create a new project use -n /path/to/project"
+        sys.exit(1)
+        
+    return options, params
+    
+if __name__ == '__main__':
+    import gtk
+    import gnome
+    
+    gnome.program_init(PROGRAM_NAME, VERSION)
+
+    options, params = parse_options()
+
+    ## Workflow setup
+    main.options = options
+    
+    for dir in main.options.workflowdir.split(';'):
+        if dir.strip() != "" and os.path.exists(dir):
+            sys.path.append(dir)
+
+    if options.list_workflows:
+        list_workflows()
+        sys.exit(0)
+
+    if options.generate_config:
+        generate_config()
+	sys.exit(0)
+
+    selected_wf = workflow.find_workflow(options.workflow) 
+    if selected_wf == None: selected_wf = workflow.EmptyWorkflow
+
+#    workflow_list = workflow.workflow_list()
+#    for wf in workflow_list:
+#        if wf.ident == options.workflow:
+#            selected_wf = wf            
+
+    main.set_workflow(selected_wf())
+    main.set_options(options)
+    app = laydi.LaydiApp()
+
+    ## Project setup
+    prjroot = params[0]
+    if not project.is_project_directory(prjroot):
+        if options.new_project:
+            project.make_project_directory(prjroot)
+        else:
+            print "error: project directory not found: %s" % prjroot
+            print "notice: use the -n option to make a new project"
+            sys.exit(2)
+    proj = project.Project(prjroot)
+    main.project = proj
+
+    main.set_application(app)
+    main.set_projectview(projectview.ProjectView(proj))
+
+    app.set_projectview(main.projectview)
+    app.show()
+    gtk.main()
+

bin/mat2ftsv

@@ -0,0 +1,37 @@
+#!/usr/bin/python
+
+import sys 
+from getopt import getopt
+
+def show_help():
+    print "mat2ftsv - Matlab matrix to laydi dataset converter."
+    print
+    print "Usage: mat2ftsv <mat-file> [<matfile> ...]"
+    print 
+    print "Description: For each mat file given as input, a ftsv file"
+    print "    will be created with the same name, but suffixed with.ftsv"
+    print "    in addition to .mat or any other suffix already on the"
+    print "    file name."
+
+options, params = getopt(sys.argv[1:], 'h', ['help'])
+
+for opt, val in options:
+    if opt in ['-h', '--help']:
+        show_help()
+        sys.exit(0)
+
+if len(params) == 0:
+    show_help()
+    sys.exit(0)
+
+from scipy import io
+from numpy import ndarray
+from laydi import dataset
+
+fn_in = params[0]
+data = io.loadmat(fn_in)
+for key, value in data.items():
+    if isinstance(value, ndarray):
+        ds = dataset.Dataset(value, name=key)
+    dataset.write_ftsv(fn_in + '.ftsv', ds)
+

bin/txt2ftsv

@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import numpy
+import os.path
+import sys
+
+from laydi import dataset
+from getopt import getopt
+
+dimension = 'dim_doe'
+output_fn = '-'
+ds_name = None
+category = False
+sparse = False
+
+def print_help():
+    print
+    print 'options:'
+    print '    -h, --help             Show this help text.'
+    print '    -c, --category         Make category dataset'
+    print '    -d, --dimension=DIM    Make output in dimension DIM'
+    print '    -n, --name=NAME        Set name of output dataset'
+    print '    -o, --output=FILE      Save output dataset in FILE'
+    print '    -s, --sparse           Save output in sparse format'
+    print
+
+def parse_options():
+    global ds_name
+    global output_fn
+
+    short_opts = 'cd:hn:o:'
+    long_opts = ['help', 'category', 'dimension', 'name', 'output', 'sparse']
+    options, params = getopt(sys.argv[1:], short_opts, long_opts)
+
+    for opt, val in options:
+        if opt in ['-h', '--help']:
+            print_help()
+            sys.exit(0)
+        elif opt in ['-c', '--category']:
+            global category
+            category = True
+        elif opt in ['-d', '--dimension']:
+            global dimension
+            dimension = val
+        elif opt in ['-n', '--name']:
+            ds_name = val
+        elif opt in ['-o', '--output']:
+            output_fn = val
+        elif opt in ['-s', '--sparse']:
+            global sparse
+            sparse = True
+    
+    if ds_name == None:
+        if output_fn != None:
+            ds_name = output_fn
+        else:
+            ds_name = 'txt2ftsv'
+
+    if len(params) == 0:
+        print_help()
+        sys.exit(1)
+
+    return params
+
+def read_file(fd):
+    lines = fd.readlines()
+    return [l.strip() for l in lines if l.strip() != '']
+    
+def build_dataset(dimension, id_lists, filenames):
+    all_ids = list(reduce(set.union, [set(x) for x in id_lists]))
+    x = numpy.zeros((len(all_ids), len(id_lists)), 'b')
+    for i, idl in enumerate(id_lists):
+        for id in idl:
+            x[all_ids.index(id),i] = True
+
+    if category:
+        ds = dataset.CategoryDataset(x, [(dimension, all_ids), ('files', filenames)], name=ds_name)
+    else:
+        ds = dataset.Dataset(x, [(dimension, all_ids), ('files', filenames)], name=ds_name)
+    return ds
+
+if __name__ == '__main__':
+    id_lists = []
+
+    filenames = parse_options()
+    for fn in filenames:
+        if os.path.exists(fn):
+            fd = open(fn)
+            id_lists.append(read_file(fd))
+            fd.close()
+        elif fn == '-':
+            id_lists.append(read_file(sys.stdin))
+
+    ds = build_dataset(dimension, id_lists, filenames)
+
+    if output_fn == '-':
+        dataset.write_ftsv(sys.stdout, ds, sp_format=sparse)
+    else:
+        dataset.write_ftsv(output_fn, ds, sp_format=sparse)
+

configure

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+
+TEMP=`getopt -o "" --long prefix:,bindir:,datadir:,pydir:,root: \
+     -n 'configure' -- "$@"`
+
+eval set -- "$TEMP"
+
+while true ; do
+	case "$1" in
+		--prefix) PREFIX=$2 ; shift 2 ;;
+		--bindir) BINDIR=$2 ; shift 2 ;;
+		--datadir) DATADIR=$2 ; shift 2 ;;
+		--pydir) PYDIR=$2 ; shift 2 ;;
+		--root) ROOT=$2 ; shift 2 ;;
+		--) shift ; break ;;
+		*) echo "Internal error!" ; exit 1 ;;
+	esac
+done
+
+#if [[ $PREFIX == "" ]] ; then PREFIX=/usr/local ; fi
+if [[ $BINDIR == "" ]] ; then BINDIR=$PREFIX/bin ; fi
+if [[ $DATADIR == "" ]] ; then DATADIR=$PREFIX/share/laydi ; fi
+if [[ $DOCDIR == "" ]] ; then DOCDIR=$PREFIX/share/doc/laydi; fi
+if [[ $PYDIR == "" ]] ; then PYDIR=$PREFIX/share/pyshared/laydi; fi
+
+m4 -D M4_PREFIX=$ROOT/$PREFIX -D M4_BINDIR=$ROOT/$BINDIR \
+   -D M4_DATADIR=$ROOT/$DATADIR -D M4_DOCDIR=$ROOT/$DOCDIR \
+   -D M4_PYDIR=$ROOT/$PYDIR Makefile.m4 > Makefile
+
+m4 -D M4_PREFIX=$ROOT/$PREFIX -D M4_BINDIR=$ROOT/$BINDIR \
+   -D M4_DATADIR=$ROOT/$DATADIR -D M4_DOCDIR=$ROOT/$DOCDIR \
+   -D M4_PYDIR=$ROOT/$PYDIR doc/Makefile.m4 > doc/Makefile
+
+m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
+   -D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
+   -D M4_PYDIR=$PYDIR laydi/paths.py.m4 > laydi/paths.py
+

debian/changelog

@@ -0,0 +1,6 @@
+laydi (0.1.0) unstable; urgency=low
+
+  * Initial packaging
+
+ -- Einar Ryeng <einarr@pvv.org>  Tue, 11 Dec 2007 16:12:59 +0100
+

debian/compat

@@ -0,0 +1 @@
+5

debian/control

@@ -0,0 +1,22 @@
+Source: laydi
+Section: science
+Priority: optional
+Maintainer: Einar Ryeng <einarr@pvv.org>
+Build-Depends: debhelper (>= 5.0.37.2), python-dateutil, python-all-dev (>= 2.3.5-7), python-central (>= 0.5), python-epydoc, python-setuptools (>=0.6b3-1) 
+Standards-Version: 3.7.2
+
+Package: laydi
+Architecture: any
+Depends: ${python:Depends},  python-numpy (>= 1:1.0.1), python-dev
+Provides: ${python:Provides}
+Description: Python library of bilinear modeling algorithms.
+ Bilinear modeling algorithms.
+
+Package: laydi-doc
+Architecture: all
+Enhances: laydi
+Description: Laydi API documentation.
+ Bilinear modeling algorithms.
+ .
+ This package contains documentation for Laydi
+

debian/copyright

@@ -0,0 +1,32 @@
+This package was debianized by Einar Ryeng <einarr@pvv.org> on
+2007-09-11.
+
+It was downloaded from https://dev.pvv.org/projects/laydi/downloads
+
+Upstream Author: Arnar Flatberg <arnar.flatberg@gmail.com>
+
+Copyright: Arnar Flatberg <arnar.flatberg@gmail.com>
+
+License:
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted under the terms of the BSD License.
+
+    THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+    ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+    OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+    LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+    SUCH DAMAGE.
+
+On Debian systems, the complete text of the BSD License can be 
+found in `/usr/share/common-licenses/BSD'.
+
+
+The Debian packaging is (C) 2007, Einar Ryeng <einarr@pvv.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+

debian/docs

@@ -0,0 +1 @@
+README

debian/rules

@@ -0,0 +1,74 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+PYVERS=$(shell pyversions -vs)
+
+configure: configure-stamp
+
+configure-stamp:
+	dh_testdir
+	touch configure-stamp
+
+build: $(PYVERS:%=build-python%)
+
+build-python%:
+	dh_testdir
+#	python$* setup.py build
+	touch $@
+
+clean: 
+	# Add here commands to clean up after the build process.
+	-rm -r build
+	dh_clean 
+
+install: build $(PYVERS:%=install-python%)
+install-python%:
+	dh_testdir
+	dh_testroot
+	dh_clean -k 
+	dh_installdirs
+	./configure --root ${CURDIR}/debian/laydi --prefix /usr --pydir /usr/share/pyshared/
+	make install
+#	python$* setup.py install --root=$(CURDIR)/debian/laydi --install-data=/usr/share/laydi
+
+	# Remove all *.pyc files, created in the postinst
+#	find $(CURDIR)/debian/python-networkx -name "*.pyc" -exec rm {} ';'
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+	make -C doc install
+#	mkdir -p $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html
+#	epydoc --html -o $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html laydi
+
+# Build architecture-dependent files here.
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs
+	dh_installexamples
+#	dh_install
+	dh_pysupport
+	dh_installman
+	dh_link
+	dh_strip
+	dh_compress
+#	dh_makeshlibs
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY:  build clean binary-indep binary-arch binary install configure

doc/Makefile.m4

@@ -0,0 +1,20 @@
+
+DOC_DIR=M4_DOCDIR
+
+all: html
+
+html:
+	@echo ----------------
+	@echo Generating epydoc html code documentation.
+	@echo See epydoc-html.log for epydoc log.
+	@echo ----------------
+	epydoc --html --inheritance listed -o html/ ../laydi 2> epydoc-html.log
+
+install: html
+	find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \;
+
+clean:
+	-rm -rf html
+	-rm epydoc-html.log
+
+	

doc/examples/gastrin-ts/VERSION

@@ -0,0 +1 @@
+Laydi project version 1

doc/gui-overview.svg

@@ -0,0 +1,215 @@
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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
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+   sodipodi:docname="gui-overview.svg"
+   inkscape:output_extension="org.inkscape.output.svg.inkscape"
+   sodipodi:docbase="/home/einarr/src/laydi/doc"
+   inkscape:export-filename="/home/einarr/src/laydi/doc/gui-overview.png"
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fluents

@@ -1,68 +0,0 @@
-#!/usr/bin/python2.4
-
-from getopt import getopt
-import sys
-from system import fluents, project, workflow
-import workflows
-
-PROGRAM_NAME = 'fluents'
-VERSION = '0.1.0'
-
-parameters = {'workflow': workflow.EmptyWorkflow}
-
-def show_help():
-    print 'fluent %s' % VERSION
-    print 'This software is released under the GNU General Public Licence'
-    print
-    print 'Usage: fluent [options]'
-    print 
-    print 'Description:'
-    print '    Fluent is a lightweight data analysis application for bilinear models.'
-    print
-    print 'Options:'
-    print '    -h --help              Show this help text'
-    print '    -l --list-workflows    Lists available workflows'
-    print '    -w --workflow=<wf>     Generates a new project based on workflow wf.'
-    print
-
-def list_workflows():
-    print 'fluent %s' % VERSION
-    print
-    print 'Workflows:'
-
-    wfs = workflow.workflow_list()
-    for wf in wfs:
-        print '    %s (%s)' % (wf.ident, wf.name)
-    print
-
-def parse_options():
-    short_opts = 'hlw:'
-    long_opts = ['help', 'list-workflows', 'workflow=']
-
-    options, params = getopt(sys.argv[1:], short_opts, long_opts)
-
-    for opt, val in options:
-        if opt in ['-h', '--help']:
-            show_help()
-            sys.exit(0)
-        elif opt in ['-l', '--list-workflows']:
-            list_workflows()
-            sys.exit(0)
-        elif opt in ['-w', '--workflow']:
-            wfs = workflow.workflow_list()
-            for wf in wfs:
-                if wf.ident == val:
-                    parameters['workflow'] = wf
-            parameters['workflow']
-
-if __name__ == '__main__':
-    parse_options()
-    
-    import gtk
-    import gnome
-    
-    gnome.program_init(PROGRAM_NAME, VERSION)
-    app = fluents.FluentApp(parameters['workflow'])
-    app.set_project(project.Project())
-    app.show()
-    gtk.main()

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+   id="svg8468"
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-   sodipodi:docbase="/home/flatberg/fluent/icons"
+   sodipodi:docbase="/home/flatberg/laydi/icons"
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-   inkscape:export-filename="/home/flatberg/fluent/icons/dataset.png"
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+   sodipodi:docbase="/home/flatberg/laydi/icons"
+   sodipodi:docname="dataset.svg"
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laydi/__init__.py

@@ -0,0 +1,3 @@
+
+import main
+

laydi/annotations.py

@@ -0,0 +1,100 @@
+
+_dim_annotation_handlers = {}
+
+def get_dim_annotations(dimname, annotation, ids):
+    """Returns a list of annotations corresponding to the given ids in 
+    dimension dimname"""
+    global _dim_annotation_handlers
+
+    if _dim_annotation_handlers.has_key(dimname):
+        return _dim_annotation_handlers[dimname].get_annotations(annotation, ids)
+    return None
+
+def set_dim_handler(dimname, handler):
+    """Set the handler for the given dimension."""
+    global _dim_annotation_handlers
+    _dim_annotation_handlers[dimname] = handler
+    
+def get_dim_handler(dimname):
+    """Get the handler for the given dimension."""
+    global _dim_annotation_handlers
+    return _dim_annotation_handlers.get(dimname, None)
+
+
+class AnnotationHandler:
+    def __init__(self):
+        pass
+
+    def get_annotations(self, annotationname, ids, default=None):
+        return None
+
+    def get_annotation_names(self):
+        return []
+
+
+class DictAnnotationHandler(AnnotationHandler):
+
+    def __init__(self, d=None):
+        if d == None:
+            d = {}
+        self._dict = d
+    
+    def get_annotations(self, annotationname, ids, default=None):
+        d = self._dict
+        retval = []
+        for id in ids:
+            if d[annotationname].has_key(id):
+                retval.append(d[annotationname][id])
+            else:
+                retval.append(default)
+        return retval
+    
+    def add_annotations(self, annotationname, d):
+        self._dict[annotationname] = d
+
+    def get_annotation_names(self):
+        return self._dict.keys()
+        
+
+def read_annotations_file(filename):
+    """Read annotations from file.
+    
+    Reads annotations from a tab delimited file of the format::
+     dimname     annotation_name1    annotation_name2 ...
+     id1         Foo                 0.43
+     id2         Bar                 0.59
+    """
+    
+    ann = DictAnnotationHandler()
+    dimname = None
+    annotation_dicts = []
+    annotation_names = []
+    
+    fd = open(filename)
+
+    ## Read the first line, which contains the dimension name and
+    ## annotation names.
+    line = fd.readline()
+    values = [x.strip() for x in line.split('\t')]
+    dimname = values[0]  
+    annotation_names = values[1:]
+    annotation_dicts = [{} for x in annotation_names]
+
+    ## Read the lines containing the annotations. The first value on
+    ## each line is an id along the dimension.
+    while line:
+        values = [x.strip() for x in line.split('\t')]
+        for i, x in enumerate(values[1:]):
+            annotation_dicts[i][values[0]] = x
+        line = fd.readline()
+
+    fd.close()
+
+    ## Add everything to the annotation object and add the object to
+    ## the specified dimension.
+    for i, a in enumerate(annotation_names):
+        ann.add_annotations(a, annotation_dicts[i])
+
+    _dim_annotation_handlers[dimname] = ann
+    return ann
+

laydi/dataset.py

@@ -0,0 +1,862 @@
+from scipy import ndarray, atleast_2d, asarray, intersect1d, zeros
+from scipy import empty, sparse, where
+from scipy import sort as array_sort
+from itertools import izip
+import shelve
+import copy
+import re
+
+class Universe(object):
+    def __init__(self, name):
+        self.name = name
+        self._ids = {}
+
+    def register(self, dim):
+        """Increase reference count for identifiers in Dimension object dim"""
+        if dim.name != self.name:
+            return
+        for i in dim:
+            self._ids[i] = self._ids.get(i, 0) + 1
+    
+    def unregister(self, dim):
+        """Update reference count for identifiers in Dimension object dim
+           Update reference count for identifiers in Dimension object dim, and remove all
+           identifiers with a reference count of 0, as they do not (by definition) exist 
+           any longer.
+        """
+        if dim.name != self.name:
+            return
+        for i in dim:
+            refcount = self._ids[i]
+            if refcount == 1:
+                self._ids.pop(i)
+            else:
+                self._ids[i] -= 1
+
+    def __str__(self):
+        return "%s: %i elements, %i references" % (self.name, len(self._ids), sum(self._ids.values()))
+
+    def __contains__(self, element):
+        return self._ids.__contains__(element)
+
+    def __len__(self):
+        return len(self._ids)
+
+    def intersection(self, dim):
+        return set(self._ids).intersection(dim.idset)
+
+
+class Dimension(object):
+    """A Dimension represents the set of identifiers an object has along an axis.
+    """
+    def __init__(self, name, ids=[]):
+        self.name = name
+        self.idset = set(ids)
+        self.idlist = list(ids)
+
+    def __getitem__(self, element):
+        return self.idlist[element]
+
+    def __getslice__(self, start, end):
+        return self.idlist[start:end]
+
+    def __contains__(self, element):
+        return self.idset.__contains__(element)
+        
+    def __str__(self):
+        return "%s: %s" % (self.name, str(self.idlist))
+
+    def __len__(self):
+        return len(self.idlist)
+
+    def __iter__(self):
+        return iter(self.idlist)
+
+    def intersection(self, dim):
+        return self.idset.intersection(dim.idset)
+
+
+class Dataset(object):
+    """The Dataset base class.
+    
+    A Dataset is an n-way array with defined string identifiers across
+    all dimensions.
+
+    example of use:
+
+    ---
+    dim_name_rows = 'rows'
+    names_rows = ('row_a','row_b')
+    ids_1 = [dim_name_rows, names_rows]
+
+    dim_name_cols = 'cols'
+    names_cols = ('col_a','col_b','col_c','col_d')
+    ids_2 = [dim_name_cols, names_cols]
+
+    Array_X = rand(2,4)
+    data = Dataset(Array_X,(ids_1,ids_2),name="Testing")
+
+    dim_names = [dim for dim in data]
+
+    column_identifiers = [id for id in data['cols'].keys()]
+    column_index = [index for index in data['cols'].values()]
+
+    'cols' in data -> True
+
+    ---
+
+    data = Dataset(rand(10,20)) (generates dims and ids (no links))
+    """
+    
+    def __init__(self, array, identifiers=None, name='Unnamed dataset'):
+        self._dims = [] #existing dimensions in this dataset
+        self._map = {} # internal mapping for dataset:  identifier <--> index
+        self._name = name
+        self._identifiers = identifiers
+        
+        if not isinstance(array, sparse.spmatrix):
+            array = atleast_2d(asarray(array))
+        # vector are column (array)
+        if array.shape[0] == 1:
+            array = array.T
+        self.shape = array.shape
+        
+        if identifiers != None:
+            self._validate_identifiers(identifiers)
+            self._set_identifiers(identifiers, self._all_dims)
+        else:
+            self._identifiers = self._create_identifiers(self.shape, self._all_dims)
+            self._set_identifiers(self._identifiers, self._all_dims)
+        self._array = array
+
+    def __iter__(self):
+        """Returns an iterator over dimensions of dataset."""
+        return self._dims.__iter__()
+
+    def __contains__(self,dim):
+        """Returns True if dim is a dimension name in dataset."""
+        # return self._dims.__contains__(dim)
+        return self._map.__contains__(dim)
+
+    def __len__(self):
+        """Returns the number of dimensions in the dataset"""
+        return len(self._map)
+
+    def __getitem__(self,dim):
+        """Return the identifers along the dimension dim."""
+        return self._map[dim]
+
+    def _create_identifiers(self, shape, all_dims):
+        """Creates dimension names and identifier names, and returns
+        identifiers."""
+        
+        dim_names = ['rows','cols'] 
+        ids = []
+        for axis, n in enumerate(shape):
+            if axis < 2:
+                dim_suggestion = dim_names[axis]
+            else:
+                dim_suggestion = 'dim'
+            dim_suggestion = self._suggest_dim_name(dim_suggestion, all_dims) 
+            identifier_creation = [str(axis) + "_" + i for i in map(str, range(n))]
+            ids.append((dim_suggestion, identifier_creation))
+            all_dims.add(dim_suggestion)
+        return ids
+
+    def _set_identifiers(self, identifiers, all_dims):
+        """Creates internal mapping of identifiers structure."""
+        for dim, ids in identifiers:
+            pos_map = ReverseDict()
+            if dim not in self._dims:
+                self._dims.append(dim)
+                all_dims.add(dim)
+            else:
+                raise ValueError, "Dimension names must be unique whitin dataset"
+            for pos, id in enumerate(ids):
+                pos_map[id] = pos
+            self._map[dim] = pos_map
+            
+    def _suggest_dim_name(self,dim_name,all_dims):
+        """Suggests a unique name for dim and returns it"""
+        c = 0
+        new_name = dim_name
+        while new_name in all_dims:
+            new_name = dim_name + "_" + str(c)
+            c += 1
+        return new_name
+        
+    def asarray(self):
+        """Returns the numeric array (data) of dataset"""
+        if isinstance(self._array, sparse.spmatrix):
+            return self._array.toarray()
+        return self._array
+
+    def set_array(self, array):
+        """Adds array as an ArrayType object.
+        A one-dim array is transformed to a two-dim array (row-vector)
+        """
+        if not isinstance(array, type(self._array)):
+            raise ValueError("Input array of type: %s does not match existing array type: %s") %(type(array), type(self._array))
+        if self.shape != array.shape:
+            raise ValueError, "Input array must be of similar dimensions as dataset"
+        self._array = atleast_2d(asarray(array))
+
+    def get_name(self):
+        """Returns dataset name"""
+        return self._name
+
+    def get_all_dims(self):
+        """Returns all dimensions in project"""
+        return self._all_dims
+
+    def get_dim_name(self, axis=None):
+        """Returns dim name for an axis, if no axis is provided it
+        returns a list of dims"""
+        if type(axis) == int:
+            return self._dims[axis]
+        else:
+            return [dim for dim in self._dims]
+
+    def common_dims(self, ds):
+        """Returns a list of the common dimensions in the two datasets."""
+        dims = self.get_dim_name()
+        ds_dims = ds.get_dim_name()
+        return [d for d in dims if d in ds_dims]
+        
+    def get_identifiers(self, dim, indices=None, sorted=False):
+        """Returns identifiers along dim, sorted by position (index)
+        is optional.
+	
+        You can optionally provide a list/ndarray of indices to get
+        only the identifiers of a given position.
+
+        Identifiers are the unique names (strings) for a variable in a
+        given dim.  Index (Indices) are the Identifiers position in a
+        matrix in a given dim.
+        """
+        if indices != None:
+            if len(indices) == 0:# if empty list or empty array
+                return []
+        if indices != None:
+            # be sure to match intersection
+            #indices = intersect1d(self.get_indices(dim),indices)
+            ids = [self._map[dim].reverse[i] for i in indices]
+	else:
+            if sorted == True:
+                ids = [self._map[dim].reverse[i] for i in array_sort(self._map[dim].values())]
+            else:
+                ids = self._map[dim].keys()
+
+        return ids
+        
+    def get_indices(self, dim, idents=None):
+        """Returns indices for identifiers along dimension.
+        You can optionally provide a list of identifiers to retrieve a
+        index subset.
+        
+        Identifiers are the unique names (strings) for a variable in a
+        given dim.  Index (Indices) are the Identifiers position in a
+        matrix in a given dim.  If none of the input identifiers are
+        found an empty index is returned
+        """
+        if not isinstance(idents, list) and not isinstance(idents, set):
+            raise ValueError("idents needs to be a list/set got: %s" %type(idents))
+        if idents == None:
+            index = array_sort(self._map[dim].values())
+        else:
+            index = [self._map[dim][key]
+                     for key in idents if self._map[dim].has_key(key)]
+        return asarray(index)        
+
+    def existing_identifiers(self, dim, idents):
+        """Filters a list of identifiers to find those that are present in the
+        dataset.
+
+        The most common use of this function is to get a list of
+        identifiers who correspond one to one with the list of indices produced
+        when get_indices is given an identifier list. That is
+        ds.get_indices(dim, idents) and ds.exisiting_identifiers(dim, idents)
+        will have the same order.
+
+        @param dim: A dimension present in the dataset.
+        @param idents: A list of identifiers along the given dimension.
+        @return: A list of identifiers in the same order as idents, but
+        without elements not present in the dataset.
+        """
+        if not isinstance(idents, list) and not isinstance(idents, set):
+            raise ValueError("idents needs to be a list/set got: %s" %type(idents))
+
+        return [key for key in idents if self._map[dim].has_key(key)]
+
+    def copy(self):
+        """ Returns deepcopy of dataset.
+        """
+        return copy.deepcopy(self)
+
+    def subdata(self, dim, idents):
+        """Returns a new dataset based on dimension and given identifiers.
+        
+        """
+        ds = self.copy()
+        indices = array_sort(ds.get_indices(dim, idents))
+        
+        idents = ds.get_identifiers(dim, indices=indices)
+        if not idents:
+            raise ValueError("No of identifers from: \n%s \nfound in %s" %(str(idents), ds._name))
+        ax = [i for i, name in enumerate(ds._dims) if name == dim][0]
+        subarr = ds._array.take(indices, ax)
+        new_indices = range(len(idents))
+        ds._map[dim] = ReverseDict(zip(idents, new_indices))
+        ds.shape = tuple(len(ds._map[d]) for d in ds._dims)
+        ds.set_array(subarr)
+        return ds
+    
+    def transpose(self):
+        """Returns a copy of transpose of a dataset.
+
+        As for the moment: only support for 2D-arrays.
+        """
+        
+        assert(len(self.shape) == 2)
+        ds = self.copy()
+        ds._array = ds._array.T
+        ds._dims.reverse()
+        ds.shape = ds._array.shape
+        return ds
+    
+    def _validate_identifiers(self, identifiers):
+        for dim_name, ids in identifiers: 
+            if len(set(ids)) != len(ids):
+                raise ValueError("Identifiers not unique in : %s" %dim_name)
+        identifier_shape = [len(i[1]) for i in identifiers]
+        if len(identifier_shape) != len(self.shape):
+            raise ValueError("Identifier list length must equal array dims")
+        for ni, na in zip(identifier_shape, self.shape):
+            if ni != na:
+                raise ValueError, "Identifier-array mismatch: %s: (idents: %s, array: %s)" %(self._name, ni, na)
+
+
+class CategoryDataset(Dataset):
+    """The category dataset class.
+
+    A dataset for representing class information as binary
+    matrices (0/1-matrices).
+
+    There is support for using a less memory demanding, sparse format. The
+    prefered (default) format for a category dataset is the compressed sparse row 
+    format (csr)
+
+    Always has linked dimension in first dim:
+    ex matrix:
+    .        go_term1    go_term2  ...
+    gene_1
+    gene_2
+    gene_3
+    .
+    .
+    .
+    
+    """
+    
+    def __init__(self, array, identifiers=None, name='C'):
+        Dataset.__init__(self, array, identifiers=identifiers, name=name)
+
+    def as_spmatrix(self):
+        if isinstance(self._array, sparse.spmatrix):
+            return self._array
+        else:
+            arr = self.asarray()
+            return sparse.csr_matrix(arr.astype('i'))
+
+    def to_spmatrix(self):
+        if isinstance(self._array, sparse.spmatrix):
+            self._array = self._array.tocsr()
+        else:
+            self._array = sparse.scr_matrix(self._array)
+
+    def as_dictlists(self):
+        """Returns data as dict of identifiers along first dim.
+
+        ex: data['gene_1'] = ['map0030','map0010', ...]
+        
+        fixme: Deprecated?
+        """
+        data = {}
+        for name, ind in self._map[self.get_dim_name(0)].items():
+            if isinstance(self._array, ndarray):
+                indices = self._array[ind,:].nonzero()[0]
+            elif isinstance(self._array, sparse.spmatrix):
+                if not isinstance(self._array, sparse.csr_matrix):
+                    array = self._array.tocsr()
+                else:
+                    array = self._array
+                indices = array[ind,:].indices
+            if len(indices) == 0: # should we allow categories with no members?
+                continue
+            data[name] = self.get_identifiers(self.get_dim_name(1), indices)
+        self._dictlists = data
+        return data
+
+    def as_selections(self):
+        """Returns data as a list of Selection objects.
+
+        The list of selections is not ordered (sorted) by any means.
+        """
+        ret_list = []
+        for cat_name, ind in self._map[self.get_dim_name(1)].items():
+            if isinstance(self._array, sparse.spmatrix):
+                if not isinstance(self._array, sparse.csc_matrix):
+                    self._array = self._array.tocsc()
+                indices = self._array[:,ind].indices
+            else:
+                indices = self._array[:,ind].nonzero()[0]
+            if len(indices) == 0:
+                continue
+            ids = self.get_identifiers(self.get_dim_name(0), indices)
+            selection = Selection(cat_name)
+            selection.select(self.get_dim_name(0), ids)
+            ret_list.append(selection)
+        return ret_list
+    
+
+class GraphDataset(Dataset):
+    """The graph dataset class.
+
+    A dataset class for representing graphs. The constructor may use an 
+    incidence matrix (possibly sparse) or (if networkx installed) a 
+    networkx.(X)Graph structure.
+    
+    If the networkx library is installed, there is support for
+    representing the graph as a networkx.Graph, or networkx.XGraph structure.
+    """
+    
+    def __init__(self, input, identifiers=None, name='A', nodepos = None):      
+        if isinstance(input, sparse.spmatrix):
+            arr = input
+        else:
+            try:
+                arr = asarray(input)
+            except:
+                raise ValueError("Could not identify input")
+        Dataset.__init__(self, array=arr, identifiers=identifiers, name=name)
+        self._graph = None
+        self.nodepos = nodepos
+        
+    def as_spmatrix(self):
+        if isinstance(self._array, sparse.spmatrix):
+            return self._array
+        else:
+            arr = self.asarray()
+            return sparse.csr_matrix(arr.astype('i'))
+
+    def to_spmatrix(self):
+        if isinstance(self._array, sparse.spmatrix):
+            self._array = self._array.tocsr()
+        else:
+            self._array = sparse.scr_matrix(self._array)
+    
+    def asnetworkx(self):
+        if self._graph != None:
+            return self._graph
+        dim0, dim1 = self.get_dim_name()
+        node_ids = self.get_identifiers(dim0, sorted=True)
+        edge_ids = self.get_identifiers(dim1, sorted=True)
+        G, weights = self._graph_from_incidence_matrix(self._array, node_ids=node_ids, edge_ids=edge_ids)
+        self._graph = G
+        return G
+        
+    def from_networkx(cls, G, node_dim, edge_dim, sp_format=True):
+        """Create graph dataset from networkx graph.
+        
+        When G is a Graph/Digraph edge identifiers will be created,
+        else (XGraoh/XDigraph) it is assumed that edge attributes are
+        the edge identifiers.
+        """
+        
+        import networkx as nx
+        n = G.number_of_nodes()
+        m = G.number_of_edges()
+        
+        if isinstance(G, nx.DiGraph):
+            G = nx.XDiGraph(G)
+        elif isinstance(G, nx.Graph):
+            G = nx.XGraph(G)
+        
+        edge_ids = [e[2] for e in G.edges()]
+        node_ids = map(str, G.nodes())
+        n2ind = {}
+        for ind, node in enumerate(node_ids):
+            n2ind[node] = ind
+        
+        if sp_format:
+            I = sparse.lil_matrix((n, m))
+        else:
+            I = zeros((m, n), dtype='i')
+        
+        for i, (h, t, eid) in enumerate(G.edges()):
+            if eid != None:
+                edge_ids[i] = eid
+            else:
+                edge_ids[i] = 'e_' + str(i)
+            hind = n2ind[str(h)]
+            tind = n2ind[str(t)]
+            I[hind, i] = 1
+            if G.is_directed():
+                I[tind, i] = -1
+            else:
+                I[tind, i] = 1
+        idents = [[node_dim, node_ids], [edge_dim, edge_ids]]
+        if G.name != '':
+            name = G.name
+        else:
+            name = 'A'
+        ds = GraphDataset(I, idents, name)
+        return ds
+    
+    from_networkx = classmethod(from_networkx)            
+    
+    def _incidence2adjacency(self, I):
+        """Incidence to adjacency matrix.
+        
+        I*I.T - eye(n)?
+        """
+        raise NotImplementedError
+    
+    def _graph_from_incidence_matrix(self, I, node_ids, edge_ids):
+        """Creates a networkx graph class from incidence
+        (possibly weighted) matrix and ordered labels.
+        
+        labels = None, results in string-numbered labels
+        """
+        try:
+            import networkx as nx
+        except:
+            print "Failed in import of NetworkX"
+            return None
+
+        m, n = I.shape
+        assert(m == len(node_ids))
+        assert(n == len(edge_ids))
+        weights = []
+        directed = False
+        G = nx.XDiGraph(name=self._name)
+        if isinstance(I, sparse.spmatrix):
+            I = I.tocsr()
+        for ename, col in izip(edge_ids, I.T):
+            if isinstance(I, sparse.spmatrix):
+                node_ind = col.indices
+                w1, w2 = col.data
+            else:
+                node_ind = where(col != 0)[0]
+                w1, w2 = col[node_ind]
+            node1 = node_ids[node_ind[0]]
+            node2 = node_ids[node_ind[1]]
+            if w1 < 0: # w1 is tail
+                directed = True
+                assert(w2 > 0 and (w1 + w2) == 0)
+                G.add_edge(node2, node1, ename)
+                weights.append(w2)
+            else: #w2 is tail or graph is undirected
+                assert(w1 > 0)
+                if w2 < 0:
+                    directed = True
+                G.add_edge(node1, node2, ename)
+                weights.append(w1)
+        if not directed:
+            G = G.to_undirected()
+        return G, asarray(weights)
+
+Dataset._all_dims = set()
+
+
+class ReverseDict(dict):
+    """A dictionary which can lookup values by key, and keys by value.
+    
+    All values and keys must be hashable, and unique.
+    
+    example:
+    >>d = ReverseDict((['a',1],['b',2]))
+    >>print d['a'] --> 1
+    >>print d.reverse[1] --> 'a'
+    """
+    def __init__(self, *args, **kw):
+        dict.__init__(self, *args, **kw)
+        self.reverse = dict([[v, k] for k, v in self.items()])
+
+    def __setitem__(self, key, value):
+        dict.__setitem__(self, key, value)
+        try:
+            self.reverse[value] = key
+        except:
+            self.reverse = {value:key}
+
+
+class Selection(dict):
+    """Handles selected identifiers along each dimension of a dataset"""
+
+    def __init__(self, title='Unnamed Selecton'):
+        self.title = title
+        
+    def __getitem__(self, key):
+        if not self.has_key(key):
+            return None
+        return dict.__getitem__(self, key)
+
+    def dims(self):
+        return self.keys()
+        
+    def axis_len(self, axis):
+        if self._selection.has_key(axis):
+            return len(self._selection[axis])
+        return 0
+
+    def select(self, axis, labels):
+        self[axis] = labels
+
+
+def write_ftsv(fd, ds, decimals=7, sep='\t', fmt=None, sp_format=True):
+    """Writes a dataset in laydi tab separated values (ftsv) form.
+    
+    @param fd: An open file descriptor to the output file.
+    @param ds: The dataset to be written. 
+    @param decimals: Number of decimals, only supported for dataset.
+    @param fmt: String formating
+    The function handles datasets of these classes: 
+    Dataset, CategoryDataset and GraphDataset
+    """
+    opened = False
+    if isinstance(fd, str):
+        fd = open(fd, 'w')
+        opened = True
+    
+    # Write header information
+    if isinstance(ds, CategoryDataset):
+        type = 'category'
+        if fmt == None:
+            fmt = '%d'
+    elif isinstance(ds, GraphDataset):
+        type = 'network'
+        if fmt == None:
+            fmt = '%d'
+    elif isinstance(ds, Dataset):
+        type = 'dataset'
+        if fmt == None:
+            fmt = '%%.%df' % decimals
+        else:
+            fmt = '%%.%d' %decimals + fmt
+    else:
+        raise Exception("Unknown object type")
+    fd.write('# type: %s' %type + '\n')
+
+    for dim in ds.get_dim_name():
+        fd.write("# dimension: %s" % dim)
+        for ident in ds.get_identifiers(dim, sorted=True):
+            fd.write(" " + ident)
+        fd.write("\n")
+
+    fd.write("# name: %s" % ds.get_name() + '\n')
+    # xy-node-positions
+    if type == 'network' and ds.nodepos != None:
+        fd.write("# nodepos:")
+        node_dim = ds.get_dim_name(0)
+        for ident in ds.get_identifiers(node_dim, sorted=True):
+            fd.write(" %s,%s" %ds.nodepos[ident])
+        fd.write("\n")
+    
+    # Write data
+    if hasattr(ds, "as_spmatrix") and sp_format == True:
+        m = ds.as_spmatrix()
+    else:
+        m = ds.asarray()
+    if isinstance(m, sparse.spmatrix):
+        _write_sparse_elements(fd, m, fmt, sep)
+    else:
+        _write_elements(fd, m, fmt, sep)
+
+    if opened:
+        fd.close()
+
+def read_ftsv(fd, sep=None):
+    """Read a dataset in laydi tab separated values (ftsv) form and return it.
+    
+    @param fd: An open file descriptor.
+    @return: A Dataset, CategoryDataset or GraphDataset depending on the information
+    read.
+    """
+    opened = False
+    if isinstance(fd, str):
+        fd = open(fd)
+        opened = True
+
+    split_re = re.compile('^#\s*(\w+)\s*:\s*(.+)')
+    dimensions = []
+    identifiers = {}
+    type = 'dataset'
+    name = 'Unnamed dataset'
+    sp_format = False
+    nodepos = None
+    # graphtype = 'graph'
+
+    # Read header lines from file.
+    line = fd.readline()
+    while line:
+        m = split_re.match(line)
+        if m:
+            key, val = m.groups()
+            
+            # The line is on the form;
+            # dimension: dimname id1 id2 id3 ...
+            if key == 'dimension':
+                values = [v.strip() for v in val.split(' ')]
+                dimensions.append(values[0])
+                identifiers[values[0]] = values[1:]
+
+            # Read type of dataset.
+            # Should be dataset, category, or network
+            elif key == 'type':
+                type = val
+            
+            elif key == 'name':
+                name = val
+            
+            # storage format
+            # if sp_format is True then use coordinate triplets
+            elif key == 'sp_format':
+                if val in ['False', 'false', '0', 'F', 'f',]:
+                    sp_format = False
+                elif val in ['True', 'true', '1', 'T', 't']:
+                    sp_format = True
+                else:
+                    raise ValueError("sp_format: %s not valid " %sp_format)
+            
+            elif key == 'nodepos':
+                node_dim = dimensions[0]
+                idents = identifiers[node_dim]
+                nodepos = {}
+                xys = val.split(" ")
+                for node_id, xy in zip(idents, xys):
+                    x, y = map(float, xy.split(","))
+                    nodepos[node_id] = (x, y)
+        
+        else:
+            break
+        line = fd.readline()
+
+    # Dimensions in the form [(dim1, [id1, id2, id3 ..) ...] 
+    dims = [(x, identifiers[x]) for x in dimensions]
+    dim_lengths = [len(identifiers[x]) for x in dimensions]
+
+    # Create matrix and assign element reader
+    if type == 'category':
+        if sp_format:
+            matrix = sparse.lil_matrix(dim_lengths)
+        else:
+            matrix = empty(dim_lengths, dtype='i')
+    else:
+        if sp_format:
+            matrix = sparse.lil_matrix(dim_lengths)
+        else:
+            matrix = empty(dim_lengths)
+
+    if sp_format:
+        matrix = _read_sparse_elements(fd, matrix)
+    else:
+        matrix = _read_elements(fd, matrix)
+    
+
+    # Create dataset of specified type
+    if type == 'category':
+        ds = CategoryDataset(matrix, dims, name)
+    elif type == 'network':
+        ds = GraphDataset(matrix, dims, name=name, nodepos=nodepos)
+    else:
+        ds = Dataset(matrix, dims, name)
+
+    if opened:
+        fd.close()
+
+    return ds
+
+def write_csv(fd, ds, decimals=7, sep='\t'):
+    """Write a dataset as comma/tab/whatever dilimited data.
+    
+    @param fd: An open file descriptor to the output file.
+    @param ds: The dataset to be written. 
+    @param decimals: Number of decimals, only supported for dataset.
+    @param sep: Value separator
+    """
+
+    ## Open file if a string is passed instead of a file descriptor
+    opened = False
+    if isinstance(fd, str):
+        fd = open(fd, 'w')
+        opened = True
+    
+    ## Get data
+    rowdim, coldim = ds.get_dim_name()
+    rowids = ds.get_identifiers(rowdim)
+    colids = ds.get_identifiers(coldim)
+    a = ds.asarray()
+    y, x = a.shape
+    fmt = '%%%if' % decimals
+
+    ## Write header
+    fd.write(rowdim)
+    fd.write(sep)
+    for i, id in enumerate(colids):
+        fd.write(id)
+        fd.write(sep)
+    fd.write('\n')
+
+    ## Write matrix data
+    for j in range(y):
+        fd.write(rowids[j])
+        fd.write(sep)
+        for i in range(x):
+            fd.write(fmt % (a[j, i],))
+            fd.write(sep)
+        fd.write('\n')
+    
+    ## If we opened the stream, close it
+    if opened:
+        fd.close()
+
+def _write_sparse_elements(fd, arr, fmt='%d', sep=None):
+    """ Sparse coordinate format.""" 
+    fd.write('# sp_format: True\n\n')
+    fmt = '%d %d ' + fmt + '\n'
+    csr = arr.tocsr()
+    for ii in xrange(csr.size):
+        ir, ic = csr.rowcol(ii)
+        data = csr.getdata(ii)
+        fd.write(fmt % (ir, ic, data))
+
+def _write_elements(fd, arr, fmt='%f', sep='\t'):
+    """Standard value separated format."""
+    fmt = fmt + sep
+    fd.write('\n')
+    y, x = arr.shape
+    for j in range(y):
+        for i in range(x):
+            fd.write(fmt %arr[j, i])
+        fd.write('\n')
+
+def _read_elements(fd, arr, sep=None):
+    line = fd.readline()
+    i = 0
+    while line:
+        values = line.split(sep)
+        for j, val in enumerate(values):
+            arr[i,j] = float(val)
+        i += 1
+        line = fd.readline()
+    return arr
+
+def _read_sparse_elements(fd, arr, sep=None):
+    line = fd.readline()
+    while line:
+        i, j, val = line.split()
+        arr[int(i),int(j)] = float(val)
+        line = fd.readline()
+    return arr.tocsr()
+

laydi/dialogs.py

@@ -4,11 +4,10 @@ import gtk
 import sys
 import os
 import gobject
-from system import logger, project, workflow
-import workflows
+import logger, projectview, workflow
 
-DATADIR = os.path.dirname(sys.modules['system'].__file__)
-GLADEFILENAME = os.path.join(DATADIR, 'fluents.glade')
+DATADIR = os.path.dirname(sys.modules['laydi'].__file__)
+GLADEFILENAME = os.path.join(DATADIR, 'laydi.glade')
 
 class CreateProjectDruid(gtk.Window):
     """A druid for creating a new project.
@@ -17,9 +16,8 @@ class CreateProjectDruid(gtk.Window):
     Workflow, and asks the user to select one of these. A new project of
     the selected class is added to the application."""
     
-    def __init__(self, app):
+    def __init__(self):
         gtk.Window.__init__(self)
-        self.app = app
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'new_project_druid')
         self.workflows = self.make_workflow_list()
         self.selected = None
@@ -63,10 +61,12 @@ class CreateProjectDruid(gtk.Window):
         
     def finish(self, *rest):
         tree, it = self['workflow_list'].get_selection().get_selected()
-        wf = self.workflows.get_value(it, 1)
-        proj = project.Project()
-        self.app.set_workflow(wf(self.app))
-        self.app.set_project(proj)
+        wf_class = self.workflows.get_value(it, 1)
+        proj = projectview.ProjectView()
+        main.set_workflow(wf_class())
+#        self.app.set_workflow(wf(self.app))
+#        self.app.set_project(proj)
+        main.set_projectview(proj)
         self.hide()
         self.destroy()
 

laydi/laydi.glade

@@ -7,7 +7,7 @@
 
 <widget class="GnomeApp" id="appwindow">
   <property name="visible">True</property>
-  <property name="title" translatable="yes">Fluent</property>
+  <property name="title" translatable="yes">Laydi</property>
   <property name="type">GTK_WINDOW_TOPLEVEL</property>
   <property name="window_position">GTK_WIN_POS_NONE</property>
   <property name="modal">False</property>
@@ -101,78 +101,6 @@
 		</widget>
 	      </child>
 
-	      <child>
-		<widget class="GtkMenuItem" id="edit1">
-		  <property name="visible">True</property>
-		  <property name="stock_item">GNOMEUIINFO_MENU_EDIT_TREE</property>
-
-		  <child>
-		    <widget class="GtkMenu" id="edit1_menu">
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="cut1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_CUT_ITEM</property>
-			  <signal name="activate" handler="on_cut1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="copy1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_COPY_ITEM</property>
-			  <signal name="activate" handler="on_copy1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="paste1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_PASTE_ITEM</property>
-			  <signal name="activate" handler="on_paste1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="clear1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_CLEAR_ITEM</property>
-			  <signal name="activate" handler="on_clear1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkSeparatorMenuItem" id="separator2">
-			  <property name="visible">True</property>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="properties1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_PROPERTIES_ITEM</property>
-			  <signal name="activate" handler="on_properties1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkSeparatorMenuItem" id="separator3">
-			  <property name="visible">True</property>
-			</widget>
-		      </child>
-
-		      <child>
-			<widget class="GtkImageMenuItem" id="preferences1">
-			  <property name="visible">True</property>
-			  <property name="stock_item">GNOMEUIINFO_MENU_PREFERENCES_ITEM</property>
-			  <signal name="activate" handler="on_preferences1_activate" last_modification_time="Thu, 13 Apr 2006 11:24:18 GMT"/>
-			</widget>
-		      </child>
-		    </widget>
-		  </child>
-		</widget>
-	      </child>
-
 	      <child>
 		<widget class="GtkMenuItem" id="view1">
 		  <property name="visible">True</property>
@@ -181,10 +109,46 @@
 		  <child>
 		    <widget class="GtkMenu" id="view1_menu">
 
+		      <child>
+			<widget class="GtkCheckMenuItem" id="navigator1">
+			  <property name="visible">True</property>
+			  <property name="label" translatable="yes">_Navigator</property>
+			  <property name="use_underline">True</property>
+			  <property name="active">True</property>
+			  <signal name="activate" handler="on_navigator1_activate" last_modification_time="Thu, 06 Dec 2007 00:03:35 GMT"/>
+			</widget>
+		      </child>
+
+		      <child>
+			<widget class="GtkCheckMenuItem" id="workflow1">
+			  <property name="visible">True</property>
+			  <property name="label" translatable="yes">_Workflow</property>
+			  <property name="use_underline">True</property>
+			  <property name="active">True</property>
+			  <signal name="activate" handler="on_workflow1_activate" last_modification_time="Thu, 06 Dec 2007 00:03:35 GMT"/>
+			</widget>
+		      </child>
+
+		      <child>
+			<widget class="GtkCheckMenuItem" id="information1">
+			  <property name="visible">True</property>
+			  <property name="label" translatable="yes">_Information</property>
+			  <property name="use_underline">True</property>
+			  <property name="active">True</property>
+			  <signal name="activate" handler="on_information1_activate" last_modification_time="Thu, 06 Dec 2007 00:03:35 GMT"/>
+			</widget>
+		      </child>
+
+		      <child>
+			<widget class="GtkSeparatorMenuItem" id="separator5">
+			  <property name="visible">True</property>
+			</widget>
+		      </child>
+
 		      <child>
 			<widget class="GtkMenuItem" id="large_view1">
 			  <property name="visible">True</property>
-			  <property name="label" translatable="yes">Large View</property>
+			  <property name="label" translatable="yes">One plot</property>
 			  <property name="use_underline">True</property>
 			  <signal name="activate" handler="on_large_view1_activate" last_modification_time="Fri, 26 May 2006 12:15:59 GMT"/>
 			  <accelerator key="plus" modifiers="GDK_CONTROL_MASK" signal="activate"/>
@@ -194,7 +158,7 @@
 		      <child>
 			<widget class="GtkMenuItem" id="small_view1">
 			  <property name="visible">True</property>
-			  <property name="label" translatable="yes">Small View</property>
+			  <property name="label" translatable="yes">All plots</property>
 			  <property name="use_underline">True</property>
 			  <signal name="activate" handler="on_small_view1_activate" last_modification_time="Fri, 26 May 2006 12:15:59 GMT"/>
 			  <accelerator key="minus" modifiers="GDK_CONTROL_MASK" signal="activate"/>
@@ -270,7 +234,7 @@
 		      <child>
 			<widget class="GtkImageMenuItem" id="index1">
 			  <property name="visible">True</property>
-			  <property name="tooltip" translatable="yes">Open the fluents documentation.</property>
+			  <property name="tooltip" translatable="yes">Open the laydi documentation.</property>
 			  <property name="label" translatable="yes">_Index</property>
 			  <property name="use_underline">True</property>
 			  <signal name="activate" handler="on_index1_activate" last_modification_time="Thu, 27 Apr 2006 09:21:48 GMT"/>
@@ -320,59 +284,13 @@
 	  <property name="shadow_type">GTK_SHADOW_OUT</property>
 
 	  <child>
-	    <widget class="GtkToolbar" id="toolbar1">
+	    <widget class="GtkToolbar" id="toolbar">
 	      <property name="visible">True</property>
 	      <property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
 	      <property name="toolbar_style">GTK_TOOLBAR_ICONS</property>
 	      <property name="tooltips">True</property>
 	      <property name="show_arrow">False</property>
 
-	      <child>
-		<widget class="GtkToolButton" id="button_new">
-		  <property name="visible">True</property>
-		  <property name="tooltip" translatable="yes">Ny fil</property>
-		  <property name="stock_id">gtk-new</property>
-		  <property name="visible_horizontal">True</property>
-		  <property name="visible_vertical">True</property>
-		  <property name="is_important">False</property>
-		  <signal name="clicked" handler="on_button_new_clicked" last_modification_time="Fri, 21 Apr 2006 13:46:38 GMT"/>
-		</widget>
-		<packing>
-		  <property name="expand">False</property>
-		  <property name="homogeneous">True</property>
-		</packing>
-	      </child>
-
-	      <child>
-		<widget class="GtkToolButton" id="toolbutton2">
-		  <property name="visible">True</property>
-		  <property name="tooltip" translatable="yes">Åpne fil</property>
-		  <property name="stock_id">gtk-open</property>
-		  <property name="visible_horizontal">True</property>
-		  <property name="visible_vertical">True</property>
-		  <property name="is_important">False</property>
-		</widget>
-		<packing>
-		  <property name="expand">False</property>
-		  <property name="homogeneous">True</property>
-		</packing>
-	      </child>
-
-	      <child>
-		<widget class="GtkToolButton" id="toolbutton3">
-		  <property name="visible">True</property>
-		  <property name="tooltip" translatable="yes">Lagre fil</property>
-		  <property name="stock_id">gtk-save</property>
-		  <property name="visible_horizontal">True</property>
-		  <property name="visible_vertical">True</property>
-		  <property name="is_important">False</property>
-		</widget>
-		<packing>
-		  <property name="expand">False</property>
-		  <property name="homogeneous">True</property>
-		</packing>
-	      </child>
-
 	      <child>
 		<widget class="GtkToolButton" id="zoom_in_button">
 		  <property name="visible">True</property>
@@ -497,12 +415,23 @@
 		      </child>
 
 		      <child>
-			<widget class="Custom" id="navigator_view">
+			<widget class="GtkScrolledWindow" id="scrolledwindow11">
 			  <property name="visible">True</property>
-			  <property name="creation_function">create_navigator_view</property>
-			  <property name="int1">0</property>
-			  <property name="int2">0</property>
-			  <property name="last_modification_time">Sat, 15 Apr 2006 12:34:23 GMT</property>
+			  <property name="can_focus">True</property>
+			  <property name="hscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
+			  <property name="vscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
+			  <property name="shadow_type">GTK_SHADOW_IN</property>
+			  <property name="window_placement">GTK_CORNER_TOP_LEFT</property>
+
+			  <child>
+			    <widget class="Custom" id="navigator_view">
+			      <property name="visible">True</property>
+			      <property name="creation_function">create_navigator_view</property>
+			      <property name="int1">0</property>
+			      <property name="int2">0</property>
+			      <property name="last_modification_time">Sat, 15 Apr 2006 12:34:23 GMT</property>
+			    </widget>
+			  </child>
 			</widget>
 			<packing>
 			  <property name="padding">0</property>
@@ -967,15 +896,16 @@ The functions of the workflow you select will be available on the right part of
 </widget>
 
 <widget class="GtkAboutDialog" id="aboutdialog">
+  <property name="border_width">5</property>
   <property name="visible">True</property>
   <property name="destroy_with_parent">True</property>
-  <property name="name" translatable="yes">Fluents</property>
-  <property name="copyright" translatable="yes">Copyright (C) 2006 the Fluents Team
+  <property name="name" translatable="yes">Laydi</property>
+  <property name="copyright" translatable="yes">Copyright (C) 2006 the Laydi Team
 Released under the GNU General Public Licence
 </property>
-  <property name="comments" translatable="yes">From WordNet (r) 2.0 [wn]: fluent (adj)
+  <property name="comments" translatable="yes">From WordNet (r) 2.0 [wn]: laydi (adj)
        
-1: easy and graceful in shape; &quot;a yacht with long, fluent curves&quot;
+1: easy and graceful in shape; &quot;a yacht with long, laydi curves&quot;
 
 2: smooth and unconstrained in movement; &quot;a long, smooth stride&quot;; &quot;the fluid motion of a cat&quot;; &quot;the liquid grace of a ballerina&quot;; &quot;liquid prose&quot; [syn:{flowing}, {fluid}, {liquid}, {smooth}]
 
@@ -983,9 +913,9 @@ Released under the GNU General Public Licence
 
 
 
-From the Fluents team: fluents (sw)
+From the Laydi team: laydi (sw)
 
-1: fluent software for lightweight data analysis.</property>
+1: laydi software for lightweight data analysis.</property>
   <property name="license" translatable="yes">GNU GENERAL PUBLIC LICENSE
 
 
@@ -1282,8 +1212,8 @@ NO WARRANTY
 END OF TERMS AND CONDITIONS
 </property>
   <property name="wrap_license">False</property>
-  <property name="website">https://dev.pvv.ntnu.no/projects/fluent</property>
-  <property name="website_label" translatable="yes">The Fluent project website</property>
+  <property name="website">https://dev.pvv.ntnu.no/projects/laydi</property>
+  <property name="website_label" translatable="yes">The Laydi project website</property>
   <property name="authors">Arnar Flatberg
 Einar Ryeng
 Truls A. Tangstad</property>

laydi/laydi.py

@@ -0,0 +1,401 @@
+#!/usr/bin/python
+
+import os
+import sys
+
+import pygtk
+pygtk.require('2.0')
+import gobject
+import gtk
+import gtk.gdk
+import gtk.glade
+import gnome
+import gnome.ui
+import scipy
+import pango
+import projectview, workflow, dataset, view, navigator, dialogs, selections, plots, main
+from logger import logger, LogView
+
+
+PROGRAM_NAME = 'laydi'
+VERSION = '0.1.0'
+DATADIR = os.path.join(main.PYDIR, 'laydi')
+#ICONDIR = os.path.join(DATADIR,"..","icons")
+ICONDIR = main.ICONDIR
+GLADEFILENAME = os.path.join(main.PYDIR, 'laydi/laydi.glade')
+_icon_mapper = {dataset.Dataset: 'dataset',
+               dataset.CategoryDataset: 'category_dataset',
+               dataset.GraphDataset: 'graph_dataset',
+               plots.Plot: 'line_plot'}
+
+class IconFactory:
+    """Factory for icons that ensures that each icon is only loaded once."""
+
+    def __init__(self, path):
+        self._path = path
+        self._icons = {}
+
+    def get(self, iconname):
+        """Returns the gdk loaded PixBuf for the given icon.
+        Reads the icon from file if necessary."""
+        
+        # if iconname isnt a string, try to autoconvert
+        if not isinstance(iconname, str):
+            for cls in _icon_mapper.keys():
+                if isinstance(iconname, cls):
+                    iconname = _icon_mapper[cls]
+        
+        if self._icons.has_key(iconname):
+            return self._icons[iconname]
+
+        icon_fname = os.path.join(self._path, '%s.png' % iconname)
+        icon = gtk.gdk.pixbuf_new_from_file(icon_fname)
+        self._icons[iconname] = icon
+        return icon
+
+icon_factory = IconFactory(ICONDIR)
+
+class TableSizeSelection(gtk.Window):
+
+    def __init__(self):
+        self._SIZE = size = 5
+        gtk.Window.__init__(self, gtk.WINDOW_POPUP)
+        self._table = gtk.Table(size, size, True)
+        self._items = []
+
+        ## Create a 3x3 table of EventBox object, doubly stored because 
+        ## gtk.Table does not support indexed retrieval.
+
+        for y in range(size):
+            line = []
+            for x in range(size):
+                ebox = gtk.EventBox()
+                ebox.add(gtk.Frame())
+                ebox.set_size_request(20, 20)
+                ebox.set_visible_window(True)
+                self._table.attach(ebox, x, x+1, y, y+1, gtk.FILL, gtk.FILL)
+                line.append(ebox)
+            self._items.append(line)
+
+        self.set_border_width(5)
+        self.add(self._table)
+        self.connect_signals()
+
+    def _get_child_pos(self, child):
+        size = self._SIZE
+        for x in range(size):
+            for y in range(size):
+                if self._items[y][x] == child:
+                    return (x, y)
+        return None
+
+    def connect_signals(self):
+        size = self._SIZE
+        for x in range(size):
+            for y in range(size):
+                self._items[y][x].add_events(gtk.gdk.ENTER_NOTIFY_MASK)
+                self._items[y][x].connect("enter-notify-event", 
+                                          self._on_enter_notify)
+                self._items[y][x].connect("button-release-event", 
+                                          self._on_button_release)
+
+    def _on_enter_notify(self, widget, event):
+        size = self._SIZE
+        x, y = self._get_child_pos(widget)
+        for i in range(size):
+            for j in range(size):
+                if i <= x and j <= y:
+                    self._items[j][i].set_state(gtk.STATE_SELECTED)
+                else:
+                    self._items[j][i].set_state(gtk.STATE_NORMAL)
+        self.x = x
+        self.y = y
+
+    def _on_button_release(self, widget, event):
+        size = self._SIZE
+        self.emit('table-size-set', self.x+1, self.y+1)
+        self.hide_all()
+
+        for x in range(size):
+            for y in range(size):
+                self._items[y][x].set_state(gtk.STATE_NORMAL)
+
+
+class ViewFrameToolButton (gtk.ToolItem):
+
+    def __init__(self):
+        gtk.ToolItem.__init__(self)
+
+        fname = os.path.join(ICONDIR, "table_size.png")
+        image = gtk.Image()
+        image.set_from_file(fname)
+
+        self._button = gtk.Button()
+        self._button.set_image(image)
+        self._button.set_property("can-focus", False)
+
+        eb = gtk.EventBox()
+        eb.add(self._button)
+        self.add(eb)
+        self._item = TableSizeSelection()
+        self._button.connect("button-press-event", self._on_show_menu)
+        image.show()
+        self._image = image
+
+        self._item.connect("table-size-set", self._on_table_size_set)
+        self._button.set_relief(gtk.RELIEF_NONE)
+        self.show_all()
+
+    def _on_show_menu(self, widget, event):
+        x, y = self._image.window.get_origin()
+        x2, y2, w, h, b = self._image.window.get_geometry()
+        
+        self._item.move(x, y+h)
+        self._item.show_all()
+
+    def _on_table_size_set(self, widget, width, height):
+        main.application['main_view'].resize_table(width, height)
+
+
+class LaydiApp:
+
+    def __init__(self): # Application variables
+        self.current_data = None
+        self._last_view = None
+        self._plot_toolbar = None
+        self._toolbar_state = None
+        
+        gtk.glade.set_custom_handler(self.custom_object_factory)
+        self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
+#        self.workflow = wf
+    
+        self.idlist_crt = selections.IdListController(self['identifier_list'])
+        self.sellist_crt = selections.SelectionListController(self['selection_tree'],
+                                                        self.idlist_crt)
+        self.dimlist_crt = selections.DimListController(self['dim_list'],
+                                                        self.sellist_crt)
+        self.sellist_crt.set_dimlist_controller(self.dimlist_crt)
+
+    def init_gui(self):
+        self['appwindow'].set_size_request(800, 600)
+
+        # Set up workflow
+        self.wf_view = workflow.WorkflowView(main.workflow)
+        self.wf_view.show()
+        self['workflow_vbox'].pack_end(self.wf_view)
+
+        self._wf_menu = workflow.WorkflowMenu(main.workflow)
+        self._wf_menu.show()
+        wf_menuitem = gtk.MenuItem('Fu_nctions')
+        wf_menuitem.set_submenu(self._wf_menu)
+        wf_menuitem.show()
+
+        self['menubar1'].insert(wf_menuitem, 2)
+
+        # Connect signals
+        signals = {'on_quit1_activate' : (gtk.main_quit),
+                   'on_appwindow_delete_event' : (gtk.main_quit),
+                   'on_zoom_in_button_clicked' : (self.on_single_view),
+                   'on_zoom_out_button_clicked' : (self.on_multiple_view),
+                   'on_new1_activate' : (self.on_create_project),
+                   'on_button_new_clicked' : (self.on_create_project),
+                   'on_workflow_refresh_clicked' : (self.on_workflow_refresh_clicked),
+                   'on_index1_activate' : (self.on_help_index),
+                   'on_about1_activate' : (self.on_help_about),
+                   'on_report_bug1_activate' : (self.on_help_report_bug),
+                   'on_small_view1_activate' : (self.on_multiple_view),
+                   'on_large_view1_activate' : (self.on_single_view),
+
+                   'on_left1_activate' : (self.on_left),
+                   'on_right1_activate' : (self.on_right),
+                   'on_up1_activate' : (self.on_up),
+                   'on_down1_activate' : (self.on_down),
+
+                   'on_navigator1_activate' : (self.on_show_navigator),
+                   'on_workflow1_activate' : (self.on_show_workflow),
+                   'on_information1_activate' : (self.on_show_infopane),
+                  }
+        self.widget_tree.signal_autoconnect(signals)
+
+        self['main_view'].connect('view-changed', self.on_view_changed)
+
+        # Log that we've set up the app now
+        logger.debug('Program started')
+
+        # Add ViewFrame table size to toolbar
+        tb = ViewFrameToolButton()
+        self['toolbar'].add(tb)
+
+    def set_projectview(self, proj):
+        logger.notice('Welcome to your new project. Grasp That Data!')
+        self.navigator_view.add_projectview(proj)
+        self.dimlist_crt.set_projectview(proj)
+        self.sellist_crt.set_projectview(proj)
+        
+    def set_workflow(self, workflow):
+        main.workflow = workflow
+        self.wf_view.set_workflow(main.workflow)
+
+    def show(self):
+        self.init_gui()
+
+    def change_plot(self, plot):
+        """Sets the plot in the currently active ViewFrame. If the plot is 
+        already shown in another ViewFrame it will be moved from there."""
+        # Set current selection in the plot before showing it.
+        plot.selection_changed(None, main.projectview.get_selection())
+
+        self['main_view'].insert_view(plot)
+        self._update_toolbar(plot)
+       
+    def change_plots(self, plots):
+        """Changes all plots.""" 
+        self['main_view'].set_all_plots(plots)
+        v = self.get_active_view_frame().get_view()
+        self._update_toolbar(v)
+
+    def get_active_view_frame(self):
+        return self['main_view'].get_active_view_frame()
+
+    def _update_toolbar(self, view):
+        """Set the plot specific toolbar to the toolbar of the currently 
+        active plot."""
+
+        # don't do anything on no change
+        if self._last_view == view:
+            return
+        self._last_view = view
+        
+        logger.debug("view changed to %s" % view)
+
+        window = self['plot_toolbar_dock']
+        if self._plot_toolbar:
+            toolbar_state = self._plot_toolbar.get_mode()
+            window.remove(self._plot_toolbar)
+        else:
+            toolbar_state = "default"
+        
+        if view:    
+            self._plot_toolbar = view.get_toolbar()
+            self._plot_toolbar.set_mode(toolbar_state)
+        else:
+            self._plot_toolbar = None
+
+        if self._plot_toolbar:
+            window.add(self._plot_toolbar)
+
+    # Methods to create GUI widgets from CustomWidgets in the glade file.
+    # The custom_object_factory calls other functions to generate specific
+    # widgets.
+
+    def custom_object_factory(self, glade, fun_name, widget_name, s1, s2, i1, i2):
+        "Called by the glade file reader to create custom GUI widgets."
+        handler = getattr(self, fun_name)
+        return handler(s1, s2, i1, i2)
+        
+    def create_logview(self, str1, str2, int1, int2):
+        self.log_view = LogView(logger)
+        self.log_view.show()
+        return self.log_view
+
+    def create_main_view(self, str1, str2, int1, int2):
+        self.main_view = view.MainView()
+        self.main_view.show()
+        return self.main_view
+
+    def create_navigator_view(self, str1, str2, int1, int2):
+        self.navigator_view = navigator.NavigatorView()
+        self.navigator_view.show()
+        return self.navigator_view
+
+    def create_dim_list(self, str1, str2, int1, int2):
+        self.dim_list = selections.DimList()
+        self.dim_list.show()
+        return self.dim_list
+    
+    def create_selection_tree(self, str1, str2, int1, int2):
+        self.selection_tree = selections.SelectionTree()
+        self.selection_tree.show()
+        return self.selection_tree
+
+    def create_identifier_list(self, str1, str2, int1, int2):
+        self.identifier_list = selections.IdentifierList()
+        self.identifier_list.show()
+        return self.identifier_list
+
+    def __getitem__(self, key):
+        return self.widget_tree.get_widget(key)
+
+    # Event handlers.
+    # These methods are called by the gtk framework in response to events and
+    # should not be called directly.
+
+    def on_single_view(self, *ignored):
+        self['main_view'].goto_large()
+
+    def on_multiple_view(self, *ignored):
+        self['main_view'].goto_small()
+
+    def on_create_project(self, *rest):
+        d = dialogs.CreateProjectDruid(self)
+        d.run()
+        
+    def on_help_about(self, *rest):
+        widget_tree = gtk.glade.XML(GLADEFILENAME, 'aboutdialog')
+        about = widget_tree.get_widget('aboutdialog')
+        about.run()
+
+    def on_help_index(self, *ignored):
+        gnome.help_display_uri('https://dev.pvv.org/projects/laydi/wiki/help')
+
+    def on_help_report_bug(self, *ignored):
+        gnome.help_display_uri('https://dev.pvv.org/projects/laydi/newticket')
+
+    def on_workflow_refresh_clicked(self, *ignored):
+        try:
+            reload(sys.modules[main.workflow.__class__.__module__])
+        except Exception, e:
+            logger.warning('Cannot reload workflow')
+            logger.warning(e)
+        else:
+            logger.notice('Successfully reloaded workflow')
+
+    def on_view_changed(self, widget, vf):
+        self._update_toolbar(vf.get_view())
+
+    def on_show_navigator(self, item):
+        if item.get_active():
+            self['data_vbox'].show()
+        else:
+            self['data_vbox'].hide()
+
+    def on_show_workflow(self, item):
+        if item.get_active():
+            self['workflow_vbox'].show()
+        else:
+            self['workflow_vbox'].hide()
+
+    def on_show_infopane(self, item):
+        if item.get_active():
+            self['bottom_notebook'].show()
+        else:
+            self['bottom_notebook'].hide()
+
+    def on_left(self, item):
+        self.main_view.move_focus_left()
+
+    def on_right(self, item):
+        self.main_view.move_focus_right()
+
+    def on_up(self, item):
+        self.main_view.move_focus_up()
+
+    def on_down(self, item):
+        self.main_view.move_focus_down()
+
+
+gobject.signal_new('table-size-set', TableSizeSelection, 
+                   gobject.SIGNAL_RUN_LAST,
+                   gobject.TYPE_NONE, 
+                   (gobject.TYPE_INT, gobject.TYPE_INT))
+

laydi/lib/R_utils.py

@@ -0,0 +1,284 @@
+"""A collection of functions that use R.
+
+Most functions use libraries from bioconductor
+
+depends on:
+(not updated)
+-- bioconductor min. install
+-- hgu133a
+-- hgu133plus2
+
+"""
+
+import scipy
+import Numeric as N
+import rpy
+silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
+
+def get_locusid(probelist=None,org="hgu133a"):
+    """Returns a dictionary of locus link id for each affy probeset
+    and reverse mapping
+
+    innput:
+    [probelist] -- probelist of affy probesets
+    [org] -- chip type (organism)
+
+    out:
+    aff2loc, loc2aff
+
+    The mapping is one-to-one for affy->locus_id
+    However, there are several affy probesets for one locus_id
+
+    From bioc-mail-archive: BioC takes the GeneBank ids associated
+    with the probes (provided by the manufacture) and then maps them
+    to Entrez Gene ids using data from UniGene, Entrez Gene, and other
+    available data sources we trust. The Entrez Gene id a probe is
+    assigned to is determined by votes from all the sources used. If
+    there is no agreement among the sources, we take the smallest
+    Entrez Gene id.
+    """
+    silent_eval("library("+org+")")
+    silent_eval('locus_ids = as.list('+org+'LOCUSID)')
+    silent_eval('pp<-as.list(locus_ids[!is.na(locus_ids)])')
+    loc_ids = rpy.r("pp")
+    for id in loc_ids:
+        loc_ids[id] = str(loc_ids[id])
+        
+    aff2loc = {}
+    if probelist:
+        for pid in probelist:
+            try:
+                aff2loc[pid]=loc_ids[pid]
+            except:
+                print "Affy probeset: %s has no locus id" %pid
+        print "\nCONVERSION SUMMARY:\n \
+        Number of probesets input %s \n \
+        Number of translated locus ids: %s \n \
+        Number of missings: %s" %(len(probelist),len(aff2loc),len(probelist)-len(aff2loc))
+    else:
+        aff2loc = loc_ids
+    # reverse mapping
+    loc2aff = {}
+    for k,v in aff2loc.items():
+        if loc2aff.has_key(v):
+            loc2aff[v].append(k)
+        else:
+            loc2aff[v]=[k]
+    
+    return aff2loc,loc2aff
+
+def get_kegg_paths(org="hgu133plus2",id_type='aff',probelist=None):
+    """Returns a dictionary of KEGG maps.
+
+    input:
+             org  --  chip_type (see bioconductor.org)
+             id_type -- id ['aff','loc']
+    
+    key: affy_id, value = list of kegg map id
+    example: '65884_at': ['00510', '00513']
+    """
+    silent_eval("library("+org+")")
+    silent_eval('xx<-as.list('+org+'PATH)')
+    silent_eval('xp <- xx[!is.na(xx)]')
+    aff2path = rpy.r("xp")
+    dummy = rpy.r("xx")
+    
+    if id_type=='loc':
+        aff2loc,loc2aff = get_locusid(org=org)
+        loc2path = {}
+        for id,path in aff2path.items():
+            if loc2path.has_key(id):
+                pp = [path.append(i) for i in loc2path[id]]
+                print "Found duplicate in path: %s" %path
+            loc2path[aff2loc[id]]=path
+        aff2path = loc2path
+    out = {}
+
+    if probelist:
+        for pid in probelist:
+            try:
+                out[pid]=aff2path[pid]
+            except:
+                print "Could not find id: %s" %pid
+    else:
+        out = aff2path
+    for k,v in out.items():
+        # if string convert tol list
+        try:
+            v + ''
+            out[k] = [v]
+        except:
+            out[k] = v
+            
+    return out
+
+def get_probe_list(org="hgu133plus2"):
+    rpy.r.library(org)
+    silent_eval('probe_list<-ls('+org+'ACCNUM )')
+    pl = rpy.r("probe_list")
+    return pl
+
+def get_GO_from_aff(org="hgu133plus2",id_type='aff',probelist=None):
+    """Returns a dictionary of GO terms.
+
+    input:
+             org  --  chip_type (see bioconductor.org)
+             id_type -- id ['aff','loc']
+    
+    key: 
+    example: '65884_at': 
+    """
+    silent_eval("library("+org+")")
+    silent_eval('xx<-as.list('+org+'GO)')
+    silent_eval('xp <- xx[!is.na(xx)]')
+    aff2path = rpy.r("xp")
+    dummy = rpy.r("xx")
+    if id_type=='loc':
+        LOC = get_locusid(org=org)
+        loc2path = {}
+        for id,path in aff2path.items():
+            if loc2path.has_key(id):
+                pp = [path.append(i) for i in loc2path[id]]
+                print "Found duplicate in path: %s" %path
+            loc2path[LOC[id]]=path
+        aff2path = loc2path
+    out = {}
+    if probelist:
+        for pid in probelist:
+            try:
+                out[pid]=aff2path[pid]
+            except:
+                print "Could not find id: %s" %pid
+    return aff2path
+
+def get_kegg_as_category(org="hgu133plus2",id_type='aff',probelist=None):
+    """Returns kegg pathway memberships in dummy (1/0) matrix (genes x maps)
+    
+    """
+    kegg = get_kegg_paths(org=org, id_type=id_type, probelist=probelist)
+    maps = set()
+    for kpth in kegg.values():
+        maps.update(kpth)
+    
+    n_maps = len(maps)
+    n_genes = len(kegg)
+    gene2index = dict(zip(kegg.keys(), range(n_genes)))
+    map2index = dict(zip(maps, range(n_maps)))
+    C = scipy.zeros((n_genes, n_maps))
+    for k,v in kegg.items():
+        for m in v:
+            C[gene2index[k], map2index[m]]=1
+        
+    return C, list(maps), kegg.keys()
+
+def impute(X, k=10, rowmax=0.5, colmax=0.8, maxp=1500, seed=362436069):
+    """
+    A function to impute missing expression data, using nearest
+    neighbor averaging. (from bioconductors impute)
+
+    input:
+
+    data: An expression matrix with genes in the rows, samples in the
+          columns
+
+       k: Number of neighbors to be used in the imputation (default=10)
+
+    rowmax: The maximum percent missing data allowed in any row (default
+          50%). For any rows with more than 'rowmax'% missing are
+          imputed using the overall mean per sample.
+
+    colmax: The maximum percent missing data allowed in any column
+          (default 80%). If any column has more than 'colmax'% missing
+          data, the program halts and reports an error.
+
+    maxp: The largest block of genes imputed using the knn algorithm
+          inside 'impute.knn' (default 1500); larger blocks are divided
+          by two-means clustering (recursively) prior to imputation. If
+          'maxp=p', only knn imputation is done
+
+    seed: The seed used for the random number generator (default
+          362436069) for reproducibility.
+
+    
+