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FIXING STUFF! 

Rename should be complete or almost so.
This commit is contained in:
Einar Ryeng 2008-12-05 22:07:56 +00:00
parent 1eabbc5c48
commit 7e6bac20e1
42 changed files with 148 additions and 148 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
Makefile.m4
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@ -10,12 +10,12 @@ install: install_laydi install_doc
install_laydi: install_laydi:
## Install binary files ## Install binary files
install -m 755 -D bin/fluents ${BIN_DIR}/fluents install -m 755 -D bin/laydi ${BIN_DIR}/laydi
install -m 755 -D bin/dataset ${BIN_DIR}/dataset install -m 755 -D bin/dataset ${BIN_DIR}/dataset
## Install library files ## Install library files
find fluents/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \; find laydi/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \;
find fluents/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \; find laydi/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \;
## Install icons ## Install icons
find icons/ -type f -name '*.png' -exec install -m 644 -D {} ${DATA_DIR}/{} \; find icons/ -type f -name '*.png' -exec install -m 644 -D {} ${DATA_DIR}/{} \;

10
README
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@ -1,8 +1,8 @@
Fluents Data Analysis Software Laydi Data Analysis Software
LICENSE LICENSE
------- -------
Fluents is relased under the terms of the GNU GPL, included in the LICENSE file Laydi is relased under the terms of the GNU GPL, included in the LICENSE file
in this directory. in this directory.
DOCUMENTATION DOCUMENTATION
@ -12,18 +12,18 @@ keyboard shortcut is listed on the wiki but it does not work in the program,
the program is right, and the wiki is wrong. the program is right, and the wiki is wrong.
That said, the next best place to look for documentation is the project wiki, That said, the next best place to look for documentation is the project wiki,
located at https://dev.pvv.ntnu.no/projects/fluents/help located at https://dev.pvv.ntnu.no/projects/laydi/help
Class documentation is in HTML form in the doc/ directory. Class documentation is in HTML form in the doc/ directory.
BUILDING BUILDING
-------- --------
Fluents is a python program, and as such, python will build compiled versions 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 of each .py file as it loads them. You do not need to explicitly compile the
program. program.
TODO TODO
---- ----
The current TODO list can be found on The current TODO list can be found on
https://dev.pvv.ntnu.no/projects/fluents/report/1 https://dev.pvv.ntnu.no/projects/laydi/report/1

6
bin/dataset
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@ -1,7 +1,7 @@
#!/usr/bin/python #!/usr/bin/python
import os,sys import os,sys
from fluents import dataset from laydi import dataset
import cfgparse, optparse import cfgparse, optparse
import re import re
@ -61,8 +61,8 @@ def list_dimension_ids(input, dimname):
print id print id
def parse_options(): def parse_options():
conf_files = ['/etc/fluentsrc', conf_files = ['/etc/laydirc',
os.path.join(os.environ['HOME'], '.fluents')] os.path.join(os.environ['HOME'], '.laydi')]
cp = cfgparse.ConfigParser() cp = cfgparse.ConfigParser()
op = optparse.OptionParser() op = optparse.OptionParser()

12
bin/laydi
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@ -3,16 +3,16 @@
from getopt import getopt from getopt import getopt
import os import os
import sys import sys
from fluents import fluents, project, workflow, main from laydi import laydi, project, workflow, main
#import workflows #import workflows
from fluents import cfgparse from laydi import cfgparse
import optparse import optparse
PROGRAM_NAME = 'laydi' PROGRAM_NAME = 'laydi'
VERSION = '0.1.0' VERSION = '0.1.0'
def list_workflows(): def list_workflows():
print 'fluents %s' % VERSION print 'laydi %s' % VERSION
print print
print 'Available workflows:' print 'Available workflows:'
@ -22,8 +22,8 @@ def list_workflows():
print print
def parse_options(): def parse_options():
conf_files = ['/etc/fluentsrc', conf_files = ['/etc/laydirc',
os.path.join(os.environ['HOME'], '.fluents')] os.path.join(os.environ['HOME'], '.laydi')]
cp = cfgparse.ConfigParser() cp = cfgparse.ConfigParser()
@ -81,7 +81,7 @@ if __name__ == '__main__':
main.set_workflow(selected_wf()) main.set_workflow(selected_wf())
main.set_options(options) main.set_options(options)
app = fluents.FluentApp() app = laydi.LaydiApp()
main.set_application(app) main.set_application(app)
main.set_project(project.Project()) main.set_project(project.Project())

4
bin/mat2ftsv
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@ -4,7 +4,7 @@ import sys
from getopt import getopt from getopt import getopt
def show_help(): def show_help():
print "mat2ftsv - Matlab matrix to fluents dataset converter." print "mat2ftsv - Matlab matrix to laydi dataset converter."
print print
print "Usage: mat2ftsv <mat-file> [<matfile> ...]" print "Usage: mat2ftsv <mat-file> [<matfile> ...]"
print print
@ -26,7 +26,7 @@ if len(params) == 0:
from scipy import io from scipy import io
from numpy import ndarray from numpy import ndarray
from fluents import dataset from laydi import dataset
fn_in = params[0] fn_in = params[0]
data = io.loadmat(fn_in) data = io.loadmat(fn_in)

2
configure vendored
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@ -34,5 +34,5 @@ m4 -D M4_PREFIX=$ROOT/$PREFIX -D M4_BINDIR=$ROOT/$BINDIR \
m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \ m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
-D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \ -D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
-D M4_PYDIR=$PYDIR fluents/paths.py.m4 > fluents/paths.py -D M4_PYDIR=$PYDIR laydi/paths.py.m4 > laydi/paths.py

2
debian/changelog vendored
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@ -1,4 +1,4 @@
fluents (0.1.0) unstable; urgency=low laydi (0.1.0) unstable; urgency=low
* Initial packaging * Initial packaging

12
debian/control vendored
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@ -1,22 +1,22 @@
Source: fluents Source: laydi
Section: science Section: science
Priority: optional Priority: optional
Maintainer: Einar Ryeng <einarr@pvv.org> 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-numpy-dev (>= 1:1.0b5), python-epydoc, python-setuptools (>=0.6b3-1) Build-Depends: debhelper (>= 5.0.37.2), python-dateutil, python-all-dev (>= 2.3.5-7), python-central (>= 0.5), python-numpy-dev (>= 1:1.0b5), python-epydoc, python-setuptools (>=0.6b3-1)
Standards-Version: 3.7.2 Standards-Version: 3.7.2
Package: fluents Package: laydi
Architecture: any Architecture: any
Depends: ${python:Depends}, python-numpy (>= 1:1.0.1), python-dev Depends: ${python:Depends}, python-numpy (>= 1:1.0.1), python-dev
Provides: ${python:Provides} Provides: ${python:Provides}
Description: Python library of bilinear modeling algorithms. Description: Python library of bilinear modeling algorithms.
Bilinear modeling algorithms. Bilinear modeling algorithms.
Package: fluents-doc Package: laydi-doc
Architecture: all Architecture: all
Enhances: fluents Enhances: laydi
Description: Fluents API documentation. Description: Laydi API documentation.
Bilinear modeling algorithms. Bilinear modeling algorithms.
. .
This package contains documentation for Fluents This package contains documentation for Laydi

2
debian/copyright vendored
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@ -1,7 +1,7 @@
This package was debianized by Einar Ryeng <einarr@pvv.org> on This package was debianized by Einar Ryeng <einarr@pvv.org> on
2007-09-11. 2007-09-11.
It was downloaded from https://dev.pvv.org/projects/fluents/downloads It was downloaded from https://dev.pvv.org/projects/laydi/downloads
Upstream Author: Arnar Flatberg <arnar.flatberg@gmail.com> Upstream Author: Arnar Flatberg <arnar.flatberg@gmail.com>

8
debian/rules vendored
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@ -36,9 +36,9 @@ install-python%:
dh_testroot dh_testroot
dh_clean -k dh_clean -k
dh_installdirs dh_installdirs
./configure --root ${CURDIR}/debian/fluents/ --prefix /usr ./configure --root ${CURDIR}/debian/laydi/ --prefix /usr
make install make install
# python$* setup.py install --root=$(CURDIR)/debian/fluents --install-data=/usr/share/fluents # python$* setup.py install --root=$(CURDIR)/debian/laydi --install-data=/usr/share/laydi
# Remove all *.pyc files, created in the postinst # Remove all *.pyc files, created in the postinst
# find $(CURDIR)/debian/python-networkx -name "*.pyc" -exec rm {} ';' # find $(CURDIR)/debian/python-networkx -name "*.pyc" -exec rm {} ';'
@ -47,8 +47,8 @@ install-python%:
# Build architecture-independent files here. # Build architecture-independent files here.
binary-indep: build install binary-indep: build install
make -C doc install make -C doc install
# mkdir -p $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html # mkdir -p $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html
# epydoc --html -o $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html fluents # epydoc --html -o $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html laydi
# Build architecture-dependent files here. # Build architecture-dependent files here.
binary-arch: build install binary-arch: build install

2
doc/Makefile.m4
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@ -8,7 +8,7 @@ html:
@echo Generating epydoc html code documentation. @echo Generating epydoc html code documentation.
@echo See epydoc-html.log for epydoc log. @echo See epydoc-html.log for epydoc log.
@echo ---------------- @echo ----------------
epydoc --html --inheritance listed -o html/ ../fluents 2> epydoc-html.log epydoc --html --inheritance listed -o html/ ../laydi 2> epydoc-html.log
install: install:
find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \; find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \;

4
icons/category_dataset.svg
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2
laydi/annotations.py
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@ -1,5 +1,5 @@
from fluents import dataset from laydi import dataset
_dim_annotation_handlers = {} _dim_annotation_handlers = {}

4
laydi/dataset.py
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@ -545,7 +545,7 @@ class Selection(dict):
def write_ftsv(fd, ds, decimals=7, sep='\t', fmt=None, sp_format=True): def write_ftsv(fd, ds, decimals=7, sep='\t', fmt=None, sp_format=True):
"""Writes a dataset in fluents tab separated values (ftsv) form. """Writes a dataset in laydi tab separated values (ftsv) form.
@param fd: An open file descriptor to the output file. @param fd: An open file descriptor to the output file.
@param ds: The dataset to be written. @param ds: The dataset to be written.
@ -607,7 +607,7 @@ def write_ftsv(fd, ds, decimals=7, sep='\t', fmt=None, sp_format=True):
fd.close() fd.close()
def read_ftsv(fd, sep=None): def read_ftsv(fd, sep=None):
"""Read a dataset in fluents tab separated values (ftsv) form and return it. """Read a dataset in laydi tab separated values (ftsv) form and return it.
@param fd: An open file descriptor. @param fd: An open file descriptor.
@return: A Dataset, CategoryDataset or GraphDataset depending on the information @return: A Dataset, CategoryDataset or GraphDataset depending on the information

4
laydi/dialogs.py
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@ -6,8 +6,8 @@ import os
import gobject import gobject
import logger, project, workflow import logger, project, workflow
DATADIR = os.path.dirname(sys.modules['fluents'].__file__) DATADIR = os.path.dirname(sys.modules['laydi'].__file__)
GLADEFILENAME = os.path.join(DATADIR, 'fluents.glade') GLADEFILENAME = os.path.join(DATADIR, 'laydi.glade')
class CreateProjectDruid(gtk.Window): class CreateProjectDruid(gtk.Window):
"""A druid for creating a new project. """A druid for creating a new project.

18
laydi/laydi.glade
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@ -234,7 +234,7 @@
<child> <child>
<widget class="GtkImageMenuItem" id="index1"> <widget class="GtkImageMenuItem" id="index1">
<property name="visible">True</property> <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="label" translatable="yes">_Index</property>
<property name="use_underline">True</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"/> <signal name="activate" handler="on_index1_activate" last_modification_time="Thu, 27 Apr 2006 09:21:48 GMT"/>
@ -899,13 +899,13 @@ The functions of the workflow you select will be available on the right part of
<property name="border_width">5</property> <property name="border_width">5</property>
<property name="visible">True</property> <property name="visible">True</property>
<property name="destroy_with_parent">True</property> <property name="destroy_with_parent">True</property>
<property name="name" translatable="yes">Fluents</property> <property name="name" translatable="yes">Laydi</property>
<property name="copyright" translatable="yes">Copyright (C) 2006 the Fluents Team <property name="copyright" translatable="yes">Copyright (C) 2006 the Laydi Team
Released under the GNU General Public Licence Released under the GNU General Public Licence
</property> </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}] 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}]
@ -913,9 +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 <property name="license" translatable="yes">GNU GENERAL PUBLIC LICENSE
@ -1212,8 +1212,8 @@ NO WARRANTY
END OF TERMS AND CONDITIONS END OF TERMS AND CONDITIONS
</property> </property>
<property name="wrap_license">False</property> <property name="wrap_license">False</property>
<property name="website">https://dev.pvv.ntnu.no/projects/fluent</property> <property name="website">https://dev.pvv.ntnu.no/projects/laydi</property>
<property name="website_label" translatable="yes">The Fluent project website</property> <property name="website_label" translatable="yes">The Laydi project website</property>
<property name="authors">Arnar Flatberg <property name="authors">Arnar Flatberg
Einar Ryeng Einar Ryeng
Truls A. Tangstad</property> Truls A. Tangstad</property>

10
laydi/laydi.py
View File

@ -19,10 +19,10 @@ from logger import logger, LogView
PROGRAM_NAME = 'laydi' PROGRAM_NAME = 'laydi'
VERSION = '0.1.0' VERSION = '0.1.0'
DATADIR = os.path.join(main.PYDIR, 'fluents') DATADIR = os.path.join(main.PYDIR, 'laydi')
#ICONDIR = os.path.join(DATADIR,"..","icons") #ICONDIR = os.path.join(DATADIR,"..","icons")
ICONDIR = main.ICONDIR ICONDIR = main.ICONDIR
GLADEFILENAME = os.path.join(main.PYDIR, 'fluents/fluents.glade') GLADEFILENAME = os.path.join(main.PYDIR, 'laydi/laydi.glade')
_icon_mapper = {dataset.Dataset: 'dataset', _icon_mapper = {dataset.Dataset: 'dataset',
dataset.CategoryDataset: 'category_dataset', dataset.CategoryDataset: 'category_dataset',
dataset.GraphDataset: 'graph_dataset', dataset.GraphDataset: 'graph_dataset',
@ -157,7 +157,7 @@ class ViewFrameToolButton (gtk.ToolItem):
main.application['main_view'].resize_table(width, height) main.application['main_view'].resize_table(width, height)
class FluentApp: class LaydiApp:
def __init__(self): # Application variables def __init__(self): # Application variables
# self.project = None # self.project = None
@ -347,10 +347,10 @@ class FluentApp:
about.run() about.run()
def on_help_index(self, *ignored): def on_help_index(self, *ignored):
gnome.help_display_uri('https://dev.pvv.org/projects/fluents/wiki/help') gnome.help_display_uri('https://dev.pvv.org/projects/laydi/wiki/help')
def on_help_report_bug(self, *ignored): def on_help_report_bug(self, *ignored):
gnome.help_display_uri('https://dev.pvv.org/projects/fluents/newticket') gnome.help_display_uri('https://dev.pvv.org/projects/laydi/newticket')
def on_workflow_refresh_clicked(self, *ignored): def on_workflow_refresh_clicked(self, *ignored):
try: try:

14
laydi/lib/blmfuncs.py
View File

@ -5,10 +5,10 @@ import copy
import pygtk import pygtk
import gtk import gtk
import gtk.glade import gtk.glade
from fluents import fluents from laydi import laydi
from fluents.workflow import Function, OptionsDialog, Options from laydi.workflow import Function, OptionsDialog, Options
from fluents.dataset import Dataset from laydi.dataset import Dataset
from fluents import plots, dataset, workflow, logger from laydi import plots, dataset, workflow, logger
import scipy import scipy
from engines import pca, pls, nipals_lpls from engines import pca, pls, nipals_lpls
from cx_stats import leverage, variances, hotelling from cx_stats import leverage, variances, hotelling
@ -763,7 +763,7 @@ class PcaOptionsDialog(OptionsDialog):
""" """
def __init__(self, data, options, input_names=['X']): def __init__(self, data, options, input_names=['X']):
OptionsDialog.__init__(self, data, options, input_names) OptionsDialog.__init__(self, data, options, input_names)
glade_file = os.path.join(fluents.DATADIR, 'pca_options.glade') glade_file = os.path.join(laydi.DATADIR, 'pca_options.glade')
notebook_name = "vbox1" notebook_name = "vbox1"
page_name = "Options" page_name = "Options"
@ -975,7 +975,7 @@ class LplsOptionsDialog(OptionsDialog):
""" """
def __init__(self, data, options, input_names=['X', 'Y', 'Z']): def __init__(self, data, options, input_names=['X', 'Y', 'Z']):
OptionsDialog.__init__(self, data, options, input_names) OptionsDialog.__init__(self, data, options, input_names)
glade_file = os.path.join(fluents.DATADIR, 'lpls_options.glade') glade_file = os.path.join(laydi.DATADIR, 'lpls_options.glade')
notebook_name = "vbox1" notebook_name = "vbox1"
page_name = "Options" page_name = "Options"
@ -1179,7 +1179,7 @@ class PlsOptionsDialog(OptionsDialog):
""" """
def __init__(self, data, options, input_names=['X', 'Y']): def __init__(self, data, options, input_names=['X', 'Y']):
OptionsDialog.__init__(self, data, options, input_names) OptionsDialog.__init__(self, data, options, input_names)
glade_file = os.path.join(fluents.DATADIR, 'pls_options.glade') glade_file = os.path.join(laydi.DATADIR, 'pls_options.glade')
notebook_name = "vbox1" notebook_name = "vbox1"
page_name = "Options" page_name = "Options"

4
laydi/lib/blmplots.py
View File

@ -7,8 +7,8 @@ fixme:
from matplotlib import cm,patches from matplotlib import cm,patches
import gtk import gtk
import fluents import laydi
from fluents import plots, main,logger from laydi import plots, main,logger
import scipy import scipy
from scipy import dot,sum,diag,arange,log,mean,newaxis,sqrt,apply_along_axis,empty from scipy import dot,sum,diag,arange,log,mean,newaxis,sqrt,apply_along_axis,empty
from scipy.stats import corrcoef from scipy.stats import corrcoef

26
laydi/navigator.py
View File

@ -2,7 +2,7 @@ import gtk
import gobject import gobject
import plots import plots
import time import time
import fluents import laydi
from logger import logger from logger import logger
import dataset, plots, project, workflow, main import dataset, plots, project, workflow, main
import scipy import scipy
@ -278,11 +278,11 @@ class NavigatorMenu(gtk.Menu):
ds = dataset.read_ftsv(filename) ds = dataset.read_ftsv(filename)
if isinstance(ds, dataset.GraphDataset): if isinstance(ds, dataset.GraphDataset):
icon = fluents.icon_factory.get("graph_dataset") icon = laydi.icon_factory.get("graph_dataset")
elif isinstance(ds, dataset.CategoryDataset): elif isinstance(ds, dataset.CategoryDataset):
icon = fluents.icon_factory.get("category_dataset") icon = laydi.icon_factory.get("category_dataset")
else: else:
icon = fluents.icon_factory.get("dataset") icon = laydi.icon_factory.get("dataset")
main.project.add_dataset(ds) main.project.add_dataset(ds)
main.project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon) main.project.data_tree_insert(None, ds.get_name(), ds, None, "black", icon)
@ -333,7 +333,7 @@ class NavigatorMenu(gtk.Menu):
def on_plot_image(self, item, navigator): def on_plot_image(self, item, navigator):
plot = plots.ImagePlot(self.dataset, name='Image Plot') plot = plots.ImagePlot(self.dataset, name='Image Plot')
icon = fluents.icon_factory.get("line_plot") icon = laydi.icon_factory.get("line_plot")
main.project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon) main.project.data_tree_insert(self.tree_iter, 'Image Plot', plot, None, "black", icon)
# fixme: image plot selections are not well defined # fixme: image plot selections are not well defined
#plot.set_selection_listener(project.set_selection) #plot.set_selection_listener(project.set_selection)
@ -342,7 +342,7 @@ class NavigatorMenu(gtk.Menu):
def on_plot_hist(self, item, navigator): def on_plot_hist(self, item, navigator):
project = main.project project = main.project
plot = plots.HistogramPlot(self.dataset, name='Histogram') plot = plots.HistogramPlot(self.dataset, name='Histogram')
icon = fluents.icon_factory.get("line_plot") icon = laydi.icon_factory.get("line_plot")
project.data_tree_insert(self.tree_iter, 'Histogram', plot, None, "black", icon) project.data_tree_insert(self.tree_iter, 'Histogram', plot, None, "black", icon)
plot.set_selection_listener(project.set_selection) plot.set_selection_listener(project.set_selection)
project._selection_observers.append(plot) project._selection_observers.append(plot)
@ -369,7 +369,7 @@ class NavigatorMenu(gtk.Menu):
ids_major[0], ids_major[1], ids_major[0], ids_major[1],
name='Scatter (%s)' % ds_major.get_name()) name='Scatter (%s)' % ds_major.get_name())
plot.add_axes_spin_buttons(len(ids_major), 0, 1) plot.add_axes_spin_buttons(len(ids_major), 0, 1)
icon = fluents.icon_factory.get("line_plot") icon = laydi.icon_factory.get("line_plot")
project.data_tree_insert(self.tree_iter, 'Scatter', plot, None, "black", icon) project.data_tree_insert(self.tree_iter, 'Scatter', plot, None, "black", icon)
plot.set_selection_listener(project.set_selection) plot.set_selection_listener(project.set_selection)
project._selection_observers.append(plot) project._selection_observers.append(plot)
@ -380,7 +380,7 @@ class NavigatorMenu(gtk.Menu):
dims = ds.get_dim_name() dims = ds.get_dim_name()
ids = ds.get_identifiers(dims[1]) ids = ds.get_identifiers(dims[1])
plot = plots.LineViewPlot(ds, name='Line (%s)' % ds.get_name()) plot = plots.LineViewPlot(ds, name='Line (%s)' % ds.get_name())
icon = fluents.icon_factory.get("line_plot") icon = laydi.icon_factory.get("line_plot")
project.data_tree_insert(self.tree_iter, 'Line view', plot, None, "black", icon) project.data_tree_insert(self.tree_iter, 'Line view', plot, None, "black", icon)
plot.set_selection_listener(project.set_selection) plot.set_selection_listener(project.set_selection)
project._selection_observers.append(plot) project._selection_observers.append(plot)
@ -389,7 +389,7 @@ class NavigatorMenu(gtk.Menu):
project = main.project project = main.project
ds = self.dataset.transpose() ds = self.dataset.transpose()
ds._name = ds._name + ".T" ds._name = ds._name + ".T"
icon = fluents.icon_factory.get(ds) icon = laydi.icon_factory.get(ds)
project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon) project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon)
def on_standardise_rows(self, item, navigator): def on_standardise_rows(self, item, navigator):
@ -398,7 +398,7 @@ class NavigatorMenu(gtk.Menu):
ds._name = self.dataset._name + ".rsc" ds._name = self.dataset._name + ".rsc"
axis = 1 axis = 1
ds._array = ds.asarray()/scipy.expand_dims(ds.asarray().std(axis), axis) ds._array = ds.asarray()/scipy.expand_dims(ds.asarray().std(axis), axis)
icon = fluents.icon_factory.get(ds) icon = laydi.icon_factory.get(ds)
project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon) project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon)
def on_standardise_cols(self, item, navigator): def on_standardise_cols(self, item, navigator):
@ -407,7 +407,7 @@ class NavigatorMenu(gtk.Menu):
ds._name = self.dataset._name + ".csc" ds._name = self.dataset._name + ".csc"
axis = 0 axis = 0
ds._array = ds.asarray()/scipy.expand_dims(ds.asarray().std(axis), axis) ds._array = ds.asarray()/scipy.expand_dims(ds.asarray().std(axis), axis)
icon = fluents.icon_factory.get(ds) icon = laydi.icon_factory.get(ds)
project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon) project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon)
def on_log(self, item, navigator): def on_log(self, item, navigator):
@ -421,7 +421,7 @@ class NavigatorMenu(gtk.Menu):
ds = self.dataset.copy() ds = self.dataset.copy()
ds._array = scipy.log(ds.asarray()) ds._array = scipy.log(ds.asarray())
icon = fluents.icon_factory.get(ds) icon = laydi.icon_factory.get(ds)
ds._name = ds._name + ".log" ds._name = ds._name + ".log"
project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon) project.data_tree_insert(self.tree_iter, ds.get_name(), ds, None, "black", icon)
@ -439,6 +439,6 @@ class NavigatorMenu(gtk.Menu):
unsel_ids = set(self.dataset.get_identifiers(dim)) - set(sel_ids) unsel_ids = set(self.dataset.get_identifiers(dim)) - set(sel_ids)
unsel_ds = self.dataset.subdata(dim, unsel_ids) unsel_ds = self.dataset.subdata(dim, unsel_ids)
icon = fluents.icon_factory.get(self.dataset) icon = laydi.icon_factory.get(self.dataset)
project.data_tree_insert(self.tree_iter, 'Selected', sel_ds, None, "black", icon) project.data_tree_insert(self.tree_iter, 'Selected', sel_ds, None, "black", icon)
project.data_tree_insert(self.tree_iter, 'Unselected', unsel_ds, None, "black", icon) project.data_tree_insert(self.tree_iter, 'Unselected', unsel_ds, None, "black", icon)

8
laydi/plots.py
View File

@ -15,7 +15,7 @@ import networkx
import scipy import scipy
from numpy import matlib from numpy import matlib
import fluents import laydi
import logger import logger
import view import view
@ -513,11 +513,11 @@ class ScatterPlot(Plot):
def is_mappable_with(self, obj): def is_mappable_with(self, obj):
"""Returns True if dataset/selection is mappable with this plot. """Returns True if dataset/selection is mappable with this plot.
""" """
if isinstance(obj, fluents.dataset.Dataset): if isinstance(obj, laydi.dataset.Dataset):
if self.current_dim in obj.get_dim_name(): if self.current_dim in obj.get_dim_name():
return True return True
elif isinstance(obj, fluents.dataset.Selection): elif isinstance(obj, laydi.dataset.Selection):
if self.current_dim in obj.get_dim_name(): if self.current_dim in obj.get_dim_name():
return True return True
@ -537,7 +537,7 @@ class ScatterPlot(Plot):
# is dataset a vector or matrix? # is dataset a vector or matrix?
if not n==1: if not n==1:
# we have a category dataset # we have a category dataset
if isinstance(data, fluents.dataset.CategoryDataset): if isinstance(data, laydi.dataset.CategoryDataset):
vec = scipy.dot(array, scipy.diag(scipy.arange(n))).sum(1) vec = scipy.dot(array, scipy.diag(scipy.arange(n))).sum(1)
else: else:
vec = array.sum(1) vec = array.sum(1)

12
laydi/project.py
View File

@ -2,7 +2,7 @@ import os
import scipy import scipy
import gobject import gobject
import gtk import gtk
import fluents import laydi
import logger, dataset, plots, main import logger, dataset, plots, main
class Project: class Project:
@ -83,7 +83,7 @@ class Project:
parent_iter = None parent_iter = None
# Add the function node to the tree # Add the function node to the tree
icon = fluents.icon_factory.get("folder_grey") icon = laydi.icon_factory.get("folder_grey")
it = self.data_tree_insert(parent_iter, fun, None, None, "black", icon) it = self.data_tree_insert(parent_iter, fun, None, None, "black", icon)
# Add all returned datasets/plots/selections # Add all returned datasets/plots/selections
@ -91,18 +91,18 @@ class Project:
# Any kind of dataset # Any kind of dataset
if isinstance(d, dataset.Dataset): if isinstance(d, dataset.Dataset):
if isinstance(d, dataset.GraphDataset): if isinstance(d, dataset.GraphDataset):
icon = fluents.icon_factory.get("graph_dataset") icon = laydi.icon_factory.get("graph_dataset")
elif isinstance(d, dataset.CategoryDataset): elif isinstance(d, dataset.CategoryDataset):
icon = fluents.icon_factory.get("category_dataset") icon = laydi.icon_factory.get("category_dataset")
else: else:
icon = fluents.icon_factory.get("dataset") icon = laydi.icon_factory.get("dataset")
self.add_dataset(d) self.add_dataset(d)
self.data_tree_insert(it, d.get_name(), d, None, "black", icon) self.data_tree_insert(it, d.get_name(), d, None, "black", icon)
# Any kind of plot # Any kind of plot
elif isinstance(d, plots.Plot): elif isinstance(d, plots.Plot):
icon = fluents.icon_factory.get("line_plot") icon = laydi.icon_factory.get("line_plot")
self.data_tree_insert(it, d.get_title(), d, None, "black", icon) self.data_tree_insert(it, d.get_title(), d, None, "black", icon)
d.set_selection_listener(self.set_selection) d.set_selection_listener(self.set_selection)
self._selection_observers.append(d) self._selection_observers.append(d)

16
laydi/view.py
View File

@ -5,7 +5,7 @@ import gtk
from matplotlib.patches import Polygon,Rectangle from matplotlib.patches import Polygon,Rectangle
from matplotlib.lines import Line2D from matplotlib.lines import Line2D
import fluents import laydi
import logger import logger
@ -212,12 +212,12 @@ class ViewFrame (gtk.Frame):
self.set_view(obj) self.set_view(obj)
self.focus() self.focus()
elif isinstance(obj, fluents.dataset.Dataset): elif isinstance(obj, laydi.dataset.Dataset):
view = self.get_view() view = self.get_view()
if view != None and view.is_mappable_with(obj): if view != None and view.is_mappable_with(obj):
view._update_color_from_dataset(obj) view._update_color_from_dataset(obj)
elif isinstance(obj, fluents.dataset.Selection): elif isinstance(obj, laydi.dataset.Selection):
view = self.get_view() view = self.get_view()
if view.is_mappable_with(obj): if view.is_mappable_with(obj):
view.selection_changed(self.current_dim, obj) view.selection_changed(self.current_dim, obj)
@ -225,7 +225,7 @@ class ViewFrame (gtk.Frame):
class MainView (gtk.Notebook): class MainView (gtk.Notebook):
"""The MainView class displays the Views in Fluents. """The MainView class displays the Views in Laydi.
MainView, of which there is normally only one instance, contains a MainView, of which there is normally only one instance, contains a
gtk.Table that holds all the visible Views, and a single ViewFrame gtk.Table that holds all the visible Views, and a single ViewFrame
@ -416,7 +416,7 @@ class MainView (gtk.Notebook):
class View (gtk.Frame): class View (gtk.Frame):
"""The base class of everything that is shown in the center view of """The base class of everything that is shown in the center view of
fluents. laydi.
Most views should rather subclass Plot, which automatically handles Most views should rather subclass Plot, which automatically handles
freezing, creates a toolbar, and sets up matplotlib Figure and Canvas freezing, creates a toolbar, and sets up matplotlib Figure and Canvas
@ -467,7 +467,7 @@ class PlotMode:
def get_icon(self): def get_icon(self):
"""Returns the icon for the PlotMode""" """Returns the icon for the PlotMode"""
image = gtk.Image() image = gtk.Image()
image.set_from_pixbuf(fluents.icon_factory.get(self.image_file)) image.set_from_pixbuf(laydi.icon_factory.get(self.image_file))
return image return image
def activate(self): def activate(self):
@ -764,7 +764,7 @@ class PlotToolbar(gtk.Toolbar):
btn = gtk.ToggleToolButton() btn = gtk.ToggleToolButton()
image = gtk.Image() image = gtk.Image()
image.set_from_pixbuf(fluents.icon_factory.get('freeze')) image.set_from_pixbuf(laydi.icon_factory.get('freeze'))
btn.set_icon_widget(image) btn.set_icon_widget(image)
btn.connect('toggled', self._on_freeze_toggle) btn.connect('toggled', self._on_freeze_toggle)
@ -850,7 +850,7 @@ class PlotToolbar(gtk.Toolbar):
dialog = gtk.FileChooserDialog('Save plot') dialog = gtk.FileChooserDialog('Save plot')
dialog.set_action(gtk.FILE_CHOOSER_ACTION_SAVE) dialog.set_action(gtk.FILE_CHOOSER_ACTION_SAVE)
dialog.add_buttons(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK) dialog.add_buttons(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK)
default_name = "fluents_image" default_name = "laydi_image"
dialog.set_current_name("%s.png" % default_name) dialog.set_current_name("%s.png" % default_name)
retval = dialog.run() retval = dialog.run()
if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]: if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]:

8
laydi/workflow.py
View File

@ -3,7 +3,7 @@ import sys
import os import os
import inspect import inspect
import logger import logger
import fluents import laydi
import main import main
def _workflow_classes(dir, modname): def _workflow_classes(dir, modname):
@ -272,12 +272,12 @@ class OptionsDialog(gtk.Dialog):
plot_treeview = gtk.TreeView(plot_list) plot_treeview = gtk.TreeView(plot_list)
# Add plots # Add plots
plot_icon = fluents.icon_factory.get('line_plot') plot_icon = laydi.icon_factory.get('line_plot')
for plt, name, use in self._options['all_plots']: for plt, name, use in self._options['all_plots']:
plot_list.append((name, use, plot_icon)) plot_list.append((name, use, plot_icon))
# Renderer for icon # Renderer for icon
plot_icon = fluents.icon_factory.get('line_plot') plot_icon = laydi.icon_factory.get('line_plot')
icon_renderer = gtk.CellRendererPixbuf() icon_renderer = gtk.CellRendererPixbuf()
icon_renderer.set_property('pixbuf', plot_icon) icon_renderer.set_property('pixbuf', plot_icon)
@ -302,7 +302,7 @@ class OptionsDialog(gtk.Dialog):
dataset_treeview = gtk.TreeView(dataset_list) dataset_treeview = gtk.TreeView(dataset_list)
# Add datasets # Add datasets
data_icon = fluents.icon_factory.get('dataset') data_icon = laydi.icon_factory.get('dataset')
for dat, name, use in self._options['all_data']: for dat, name, use in self._options['all_data']:
dataset_list.append((name, use, data_icon)) dataset_list.append((name, use, data_icon))

4
run-laydi
View File

@ -1,8 +1,8 @@
#!/bin/sh #!/bin/sh
## To be able to run fluents without installing it, we have to set ## To be able to run laydi without installing it, we have to set
## PYTHONPATH. ## PYTHONPATH.
export PYTHONPATH=$PYTHONPATH:.:./workflows export PYTHONPATH=$PYTHONPATH:.:./workflows
./bin/fluents $@ ./bin/laydi $@

2
scripts/README
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@ -1,6 +1,6 @@
This directory and its subdirectories are intended for small scripts that are This directory and its subdirectories are intended for small scripts that are
not considered parts of fluents proper. They are included because they do not considered parts of laydi proper. They are included because they do
useful tings in preprocessing data, often for a specific use (e.g. microarray useful tings in preprocessing data, often for a specific use (e.g. microarray
analysis with gene ontology background information). analysis with gene ontology background information).

2
scripts/geneontology/entrez-go-mapping
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@ -52,7 +52,7 @@ def parse_options():
help="Output annotations in the cellular component tree.", help="Output annotations in the cellular component tree.",
action="store_true", default=False) action="store_true", default=False)
op.add_option('-d', '--output-dataset', op.add_option('-d', '--output-dataset',
help="Export as ftsv (Fluents dataset) file.") help="Export as ftsv (Laydi dataset) file.")
op.add_option('-m', '--molecular-function', dest="mf", op.add_option('-m', '--molecular-function', dest="mf",
help="Output annotations in the molecular function tree.", help="Output annotations in the molecular function tree.",
action="store_true", default=False) action="store_true", default=False)

2
scripts/geneontology/go-gene-matrix
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@ -3,7 +3,7 @@
import os, sys import os, sys
import getopt import getopt
sys.path.append('../..') sys.path.append('../..')
from fluents import dataset from laydi import dataset
import numpy import numpy
max_val = numpy.inf max_val = numpy.inf

2
scripts/lpls/lpls.py
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@ -4,7 +4,7 @@ import matplotlib
from scipy import * from scipy import *
from scipy.linalg import inv,norm from scipy.linalg import inv,norm
sys.path.append("../../fluents/lib") sys.path.append("../../laydi/lib")
import select_generators import select_generators
def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], scale='scores', verbose=True): def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], scale='scores', verbose=True):

6
scripts/lpls/run_smoker.py
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@ -6,9 +6,9 @@ from scipy.linalg import norm
from lpls import correlation_loadings from lpls import correlation_loadings
import rpy_go import rpy_go
sys.path.append("../../fluents") # home of dataset sys.path.append("../../laydi") # home of dataset
sys.path.append("../../fluents/lib") # home of cx_stats sys.path.append("../../laydi/lib") # home of cx_stats
sys.path.append("/home/flatberg/fluents/scripts/lpls") sys.path.append("/home/flatberg/laydi/scripts/lpls")
sys.path.append("/home/flatberg/pyblm/") sys.path.append("/home/flatberg/pyblm/")
import dataset import dataset
import cx_stats import cx_stats

8
setup.py
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@ -21,15 +21,15 @@ Programming Language :: Python
Topic :: Scientific/Engineering Topic :: Scientific/Engineering
""" """
from fluents.fluents import VERSION from laydi.laydi import VERSION
def configuration(parent_package='', top_path=None): def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path) config = Configuration('', parent_package, top_path)
config.add_data_dir('tests') config.add_data_dir('tests')
config.add_scripts(['bin/fluents', 'bin/dataset']) config.add_scripts(['bin/laydi', 'bin/dataset'])
config.add_data_dir('icons') config.add_data_dir('icons')
config.add_subpackage('fluents') config.add_subpackage('laydi')
return config return config
if __name__ == "__main__": if __name__ == "__main__":
@ -39,7 +39,7 @@ if __name__ == "__main__":
config['author_email'] = 'einarr@pvv.org' config['author_email'] = 'einarr@pvv.org'
# config['short_description'] = short_description # config['short_description'] = short_description
config['long_description'] = long_description config['long_description'] = long_description
config['url'] = 'https://dev.pvv.org/projects/fluents' config['url'] = 'https://dev.pvv.org/projects/laydi'
config['version'] = VERSION config['version'] = VERSION
config['license'] = 'GPL' config['license'] = 'GPL'
config['platforms'] = ['Linux'] config['platforms'] = ['Linux']

2
test/laydi/annotationtest.py
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@ -2,7 +2,7 @@
import unittest import unittest
import sys import sys
sys.path.append('../../') sys.path.append('../../')
from fluents import annotations from laydi import annotations
class AnnotationsTest(unittest.TestCase): class AnnotationsTest(unittest.TestCase):

8
workflows/demo.py
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@ -6,8 +6,8 @@ import cPickle
import scipy import scipy
import networkx as nx import networkx as nx
from fluents import logger,plots,workflow,dataset,main from laydi import logger,plots,workflow,dataset,main
from fluents.lib import blmfuncs,nx_utils,cx_utils from laydi.lib import blmfuncs,nx_utils,cx_utils
import gobrowser import gobrowser
@ -363,7 +363,7 @@ class MapGene2GO(workflow.Function):
workflow.Function.__init__(self, 'gene2go', 'gene->GO') workflow.Function.__init__(self, 'gene2go', 'gene->GO')
# load data at init # load data at init
try: try:
fname = "/home/flatberg/fluents/data/gene2go.pcl" fname = "/home/flatberg/laydi/data/gene2go.pcl"
self._gene2go = cPickle.load(open(fname)) self._gene2go = cPickle.load(open(fname))
except: except:
logger.log("notice", "could not load mapping") logger.log("notice", "could not load mapping")
@ -395,7 +395,7 @@ class MapGO2Gene(workflow.Function):
workflow.Function.__init__(self, 'go2gene', 'GO->gene') workflow.Function.__init__(self, 'go2gene', 'GO->gene')
# load data at init # load data at init
try: try:
fname = "/home/flatberg/fluents/data/go2gene.pcl" fname = "/home/flatberg/laydi/data/go2gene.pcl"
self._go2gene = cPickle.load(open(fname)) self._go2gene = cPickle.load(open(fname))
except: except:
logger.log("notice", "could not load mapping") logger.log("notice", "could not load mapping")

6
workflows/go_workflow.py
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@ -1,6 +1,6 @@
import gtk import gtk
from fluents import dataset, logger, plots, workflow, fluents, project from laydi import dataset, logger, plots, workflow, laydi, project
from fluents.lib import blmfuncs from laydi.lib import blmfuncs
import geneontology import geneontology
#import gostat #import gostat
from scipy import array, randn, log, ones, zeros from scipy import array, randn, log, ones, zeros
@ -245,7 +245,7 @@ class LoadGOFunction(workflow.Function):
browser = GeneOntologyTree(go) browser = GeneOntologyTree(go)
label = gtk.Label('_Gene Ontology') label = gtk.Label('_Gene Ontology')
label.set_use_underline(True) label.set_use_underline(True)
fluents.app['bottom_notebook'].append_page(browser, label) laydi.app['bottom_notebook'].append_page(browser, label)
class LoadTextDatasetFunction(workflow.Function): class LoadTextDatasetFunction(workflow.Function):

8
workflows/gobrowser.py
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@ -1,6 +1,6 @@
import gtk import gtk
from fluents import dataset, logger, plots, workflow, fluents, project, view, main from laydi import dataset, logger, plots, workflow, laydi, project, view, main
import geneontology import geneontology
from matplotlib.nxutils import points_inside_poly from matplotlib.nxutils import points_inside_poly
import matplotlib import matplotlib
@ -243,7 +243,7 @@ class LoadGOFunction(workflow.Function):
browser = GeneOntologyTree(go) browser = GeneOntologyTree(go)
label = gtk.Label('_Gene Ontology') label = gtk.Label('_Gene Ontology')
label.set_use_underline(True) label.set_use_underline(True)
fluents.app['bottom_notebook'].append_page(browser, label) laydi.app['bottom_notebook'].append_page(browser, label)
class LoadAnnotationsFunction(workflow.Function): class LoadAnnotationsFunction(workflow.Function):
@ -699,7 +699,7 @@ class DagPlot(plots.Plot):
def is_mappable_with(self, obj): def is_mappable_with(self, obj):
"""Returns True if dataset/selection is mappable with this plot. """Returns True if dataset/selection is mappable with this plot.
""" """
if isinstance(obj, fluents.dataset.Dataset): if isinstance(obj, laydi.dataset.Dataset):
if self.current_dim in obj.get_dim_name(): if self.current_dim in obj.get_dim_name():
return True return True
return False return False
@ -718,7 +718,7 @@ class DagPlot(plots.Plot):
# is dataset a vector or matrix? # is dataset a vector or matrix?
if not n==1: if not n==1:
# we have a category dataset # we have a category dataset
if isinstance(ds, fluents.dataset.CategoryDataset): if isinstance(ds, laydi.dataset.CategoryDataset):
vec = dot(array, diag(arange(n))).sum(1) vec = dot(array, diag(arange(n))).sum(1)
else: else:
vec = array.sum(1) vec = array.sum(1)

10
workflows/smokers.py
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@ -3,8 +3,8 @@ import os.path
import webbrowser import webbrowser
import cPickle import cPickle
from fluents import logger, plots,workflow,dataset,main from laydi import logger, plots,workflow,dataset,main
from fluents.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
import gobrowser, geneontology import gobrowser, geneontology
import scipy import scipy
import networkx as nx import networkx as nx
@ -103,7 +103,7 @@ class DatasetLoadFunctionCYCLE(workflow.Function):
workflow.Function.__init__(self, 'load_data', 'Cycle') workflow.Function.__init__(self, 'load_data', 'Cycle')
def run(self): def run(self):
filename='fluents/data/CYCLE' filename='laydi/data/CYCLE'
if filename: if filename:
return dataset.from_file(filename) return dataset.from_file(filename)
@ -419,7 +419,7 @@ class MapGene2GO(workflow.Function):
workflow.Function.__init__(self, 'gene2go', 'gene->GO') workflow.Function.__init__(self, 'gene2go', 'gene->GO')
# load data at init # load data at init
try: try:
fname = "/home/flatberg/fluents/data/gene2go.pcl" fname = "/home/flatberg/laydi/data/gene2go.pcl"
self._gene2go = cPickle.load(open(fname)) self._gene2go = cPickle.load(open(fname))
except: except:
logger.log("notice", "could not load mapping") logger.log("notice", "could not load mapping")
@ -451,7 +451,7 @@ class MapGO2Gene(workflow.Function):
workflow.Function.__init__(self, 'go2gene', 'GO->gene') workflow.Function.__init__(self, 'go2gene', 'GO->gene')
# load data at init # load data at init
try: try:
fname = "/home/flatberg/fluents/data/go2gene.pcl" fname = "/home/flatberg/laydi/data/go2gene.pcl"
self._go2gene = cPickle.load(open(fname)) self._go2gene = cPickle.load(open(fname))
except: except:
logger.log("notice", "could not load mapping") logger.log("notice", "could not load mapping")

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workflows/test_workflow.py
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@ -1,5 +1,5 @@
import gtk import gtk
from fluents import dataset, logger, plots, workflow from laydi import dataset, logger, plots, workflow
#import geneontology #import geneontology
#import gostat #import gostat
from scipy import array, randn, log, ones from scipy import array, randn, log, ones