parent
1eabbc5c48
commit
7e6bac20e1
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@ -10,12 +10,12 @@ install: install_laydi install_doc
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install_laydi:
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## Install binary files
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install -m 755 -D bin/fluents ${BIN_DIR}/fluents
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install -m 755 -D bin/laydi ${BIN_DIR}/laydi
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install -m 755 -D bin/dataset ${BIN_DIR}/dataset
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## Install library files
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find fluents/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \;
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find fluents/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \;
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find laydi/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \;
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find laydi/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \;
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## Install icons
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find icons/ -type f -name '*.png' -exec install -m 644 -D {} ${DATA_DIR}/{} \;
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10
README
10
README
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@ -1,8 +1,8 @@
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Fluents Data Analysis Software
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Laydi Data Analysis Software
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LICENSE
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-------
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Fluents is relased under the terms of the GNU GPL, included in the LICENSE file
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Laydi is relased under the terms of the GNU GPL, included in the LICENSE file
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in this directory.
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DOCUMENTATION
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@ -12,18 +12,18 @@ keyboard shortcut is listed on the wiki but it does not work in the program,
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the program is right, and the wiki is wrong.
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That said, the next best place to look for documentation is the project wiki,
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located at https://dev.pvv.ntnu.no/projects/fluents/help
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located at https://dev.pvv.ntnu.no/projects/laydi/help
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Class documentation is in HTML form in the doc/ directory.
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BUILDING
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--------
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Fluents is a python program, and as such, python will build compiled versions
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Laydi is a python program, and as such, python will build compiled versions
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of each .py file as it loads them. You do not need to explicitly compile the
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program.
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TODO
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----
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The current TODO list can be found on
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https://dev.pvv.ntnu.no/projects/fluents/report/1
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https://dev.pvv.ntnu.no/projects/laydi/report/1
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@ -1,7 +1,7 @@
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#!/usr/bin/python
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import os,sys
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from fluents import dataset
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from laydi import dataset
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import cfgparse, optparse
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import re
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@ -61,8 +61,8 @@ def list_dimension_ids(input, dimname):
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print id
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def parse_options():
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conf_files = ['/etc/fluentsrc',
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os.path.join(os.environ['HOME'], '.fluents')]
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conf_files = ['/etc/laydirc',
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os.path.join(os.environ['HOME'], '.laydi')]
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cp = cfgparse.ConfigParser()
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op = optparse.OptionParser()
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12
bin/laydi
12
bin/laydi
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@ -3,16 +3,16 @@
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from getopt import getopt
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import os
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import sys
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from fluents import fluents, project, workflow, main
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from laydi import laydi, project, workflow, main
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#import workflows
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from fluents import cfgparse
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from laydi import cfgparse
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import optparse
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PROGRAM_NAME = 'laydi'
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VERSION = '0.1.0'
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def list_workflows():
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print 'fluents %s' % VERSION
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print 'laydi %s' % VERSION
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print
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print 'Available workflows:'
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@ -22,8 +22,8 @@ def list_workflows():
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print
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def parse_options():
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conf_files = ['/etc/fluentsrc',
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os.path.join(os.environ['HOME'], '.fluents')]
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conf_files = ['/etc/laydirc',
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os.path.join(os.environ['HOME'], '.laydi')]
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cp = cfgparse.ConfigParser()
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@ -81,7 +81,7 @@ if __name__ == '__main__':
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main.set_workflow(selected_wf())
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main.set_options(options)
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app = fluents.FluentApp()
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app = laydi.LaydiApp()
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main.set_application(app)
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main.set_project(project.Project())
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@ -4,7 +4,7 @@ import sys
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from getopt import getopt
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def show_help():
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print "mat2ftsv - Matlab matrix to fluents dataset converter."
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print "mat2ftsv - Matlab matrix to laydi dataset converter."
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print
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print "Usage: mat2ftsv <mat-file> [<matfile> ...]"
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print
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@ -26,7 +26,7 @@ if len(params) == 0:
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from scipy import io
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from numpy import ndarray
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from fluents import dataset
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from laydi import dataset
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fn_in = params[0]
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data = io.loadmat(fn_in)
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@ -34,5 +34,5 @@ m4 -D M4_PREFIX=$ROOT/$PREFIX -D M4_BINDIR=$ROOT/$BINDIR \
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m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
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-D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
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-D M4_PYDIR=$PYDIR fluents/paths.py.m4 > fluents/paths.py
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-D M4_PYDIR=$PYDIR laydi/paths.py.m4 > laydi/paths.py
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@ -1,4 +1,4 @@
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fluents (0.1.0) unstable; urgency=low
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laydi (0.1.0) unstable; urgency=low
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* Initial packaging
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@ -1,22 +1,22 @@
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Source: fluents
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Source: laydi
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Section: science
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Priority: optional
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Maintainer: Einar Ryeng <einarr@pvv.org>
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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)
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Standards-Version: 3.7.2
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Package: fluents
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Package: laydi
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Architecture: any
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Depends: ${python:Depends}, python-numpy (>= 1:1.0.1), python-dev
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Provides: ${python:Provides}
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Description: Python library of bilinear modeling algorithms.
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Bilinear modeling algorithms.
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Package: fluents-doc
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Package: laydi-doc
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Architecture: all
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Enhances: fluents
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Description: Fluents API documentation.
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Enhances: laydi
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Description: Laydi API documentation.
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Bilinear modeling algorithms.
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.
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This package contains documentation for Fluents
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This package contains documentation for Laydi
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@ -1,7 +1,7 @@
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This package was debianized by Einar Ryeng <einarr@pvv.org> on
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2007-09-11.
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It was downloaded from https://dev.pvv.org/projects/fluents/downloads
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It was downloaded from https://dev.pvv.org/projects/laydi/downloads
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Upstream Author: Arnar Flatberg <arnar.flatberg@gmail.com>
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@ -36,9 +36,9 @@ install-python%:
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dh_testroot
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dh_clean -k
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dh_installdirs
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./configure --root ${CURDIR}/debian/fluents/ --prefix /usr
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./configure --root ${CURDIR}/debian/laydi/ --prefix /usr
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make install
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# python$* setup.py install --root=$(CURDIR)/debian/fluents --install-data=/usr/share/fluents
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# python$* setup.py install --root=$(CURDIR)/debian/laydi --install-data=/usr/share/laydi
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# Remove all *.pyc files, created in the postinst
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# find $(CURDIR)/debian/python-networkx -name "*.pyc" -exec rm {} ';'
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@ -47,8 +47,8 @@ install-python%:
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# Build architecture-independent files here.
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binary-indep: build install
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make -C doc install
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# mkdir -p $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html
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# epydoc --html -o $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html fluents
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# mkdir -p $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html
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# epydoc --html -o $(CURDIR)/debian/laydi-doc/usr/share/doc/laydi-doc/html laydi
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# Build architecture-dependent files here.
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binary-arch: build install
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@ -8,7 +8,7 @@ html:
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@echo Generating epydoc html code documentation.
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@echo See epydoc-html.log for epydoc log.
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@echo ----------------
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epydoc --html --inheritance listed -o html/ ../fluents 2> epydoc-html.log
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epydoc --html --inheritance listed -o html/ ../laydi 2> epydoc-html.log
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install:
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find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \;
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@ -14,9 +14,9 @@
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id="svg8468"
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/flatberg/fluent/icons"
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sodipodi:docbase="/home/flatberg/laydi/icons"
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sodipodi:docname="category_dataset.svg"
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inkscape:export-filename="/home/flatberg/fluent/icons/category_dataset.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/category_dataset.png"
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inkscape:export-xdpi="90"
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inkscape:export-ydpi="90">
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<defs
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Before Width: | Height: | Size: 7.3 KiB After Width: | Height: | Size: 7.3 KiB |
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id="svg1617"
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/flatberg/fluent/icons"
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sodipodi:docbase="/home/flatberg/laydi/icons"
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sodipodi:docname="dataset.svg"
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inkscape:export-filename="/home/flatberg/fluent/icons/dataset.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/dataset.png"
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inkscape:export-xdpi="90"
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inkscape:export-ydpi="90">
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<defs
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Before Width: | Height: | Size: 7.8 KiB After Width: | Height: | Size: 7.8 KiB |
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id="svg8468"
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/flatberg/fluent/icons"
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sodipodi:docbase="/home/flatberg/laydi/icons"
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sodipodi:docname="graph_dataset.svg"
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inkscape:export-filename="/home/flatberg/fluent/icons/graph_dataset.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/graph_dataset.png"
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inkscape:export-xdpi="90"
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inkscape:export-ydpi="90">
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<defs
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@ -13,9 +13,9 @@
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id="svg1337"
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/flatberg/fluents/icons"
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sodipodi:docbase="/home/flatberg/laydi/icons"
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sodipodi:docname="lasso.svg"
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inkscape:export-filename="/home/flatberg/fluents/icons/lasso.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/lasso.png"
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inkscape:export-xdpi="37.5"
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inkscape:export-ydpi="37.5">
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<defs
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Before Width: | Height: | Size: 2.3 KiB After Width: | Height: | Size: 2.3 KiB |
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id="svg8468"
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/flatberg/fluent/icons"
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sodipodi:docbase="/home/flatberg/laydi/icons"
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sodipodi:docname="line_plot.svg"
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inkscape:export-filename="/home/flatberg/fluent/icons/line_plot.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/line_plot.png"
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inkscape:export-xdpi="90"
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inkscape:export-ydpi="90">
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<defs
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id="path3482"
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sodipodi:nodetypes="csssscs"
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inkscape:export-filename="/home/flatberg/fluent/icons/line_plot.png"
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inkscape:export-filename="/home/flatberg/laydi/icons/line_plot.png"
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inkscape:export-xdpi="130.40465"
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inkscape:export-ydpi="130.40465" />
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Before Width: | Height: | Size: 8.0 KiB After Width: | Height: | Size: 8.0 KiB |
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sodipodi:version="0.32"
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inkscape:version="0.43"
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sodipodi:docbase="/home/einarr/src/laydi/icons"
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sodipodi:docname="table_size.svg">
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<defs
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|
||||
inkscape:export-ydpi="3.4739451" />
|
||||
<rect
|
||||
|
|
|
|||
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 12 KiB |
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
from fluents import dataset
|
||||
from laydi import dataset
|
||||
|
||||
_dim_annotation_handlers = {}
|
||||
|
||||
|
|
|
|||
|
|
@ -545,7 +545,7 @@ class Selection(dict):
|
|||
|
||||
|
||||
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 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()
|
||||
|
||||
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.
|
||||
@return: A Dataset, CategoryDataset or GraphDataset depending on the information
|
||||
|
|
|
|||
|
|
@ -6,8 +6,8 @@ import os
|
|||
import gobject
|
||||
import logger, project, workflow
|
||||
|
||||
DATADIR = os.path.dirname(sys.modules['fluents'].__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.
|
||||
|
|
|
|||
|
|
@ -234,7 +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"/>
|
||||
|
|
@ -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="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; "a yacht with long, fluent curves"
|
||||
1: easy and graceful in shape; "a yacht with long, laydi curves"
|
||||
|
||||
2: smooth and unconstrained in movement; "a long, smooth stride"; "the fluid motion of a cat"; "the liquid grace of a ballerina"; "liquid prose" [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
|
||||
|
||||
|
||||
|
|
@ -1212,8 +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>
|
||||
|
|
|
|||
|
|
@ -19,10 +19,10 @@ from logger import logger, LogView
|
|||
|
||||
PROGRAM_NAME = 'laydi'
|
||||
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 = 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',
|
||||
dataset.CategoryDataset: 'category_dataset',
|
||||
dataset.GraphDataset: 'graph_dataset',
|
||||
|
|
@ -157,7 +157,7 @@ class ViewFrameToolButton (gtk.ToolItem):
|
|||
main.application['main_view'].resize_table(width, height)
|
||||
|
||||
|
||||
class FluentApp:
|
||||
class LaydiApp:
|
||||
|
||||
def __init__(self): # Application variables
|
||||
# self.project = None
|
||||
|
|
@ -347,10 +347,10 @@ class FluentApp:
|
|||
about.run()
|
||||
|
||||
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):
|
||||
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):
|
||||
try:
|
||||
|
|
|
|||
|
|
@ -5,10 +5,10 @@ import copy
|
|||
import pygtk
|
||||
import gtk
|
||||
import gtk.glade
|
||||
from fluents import fluents
|
||||
from fluents.workflow import Function, OptionsDialog, Options
|
||||
from fluents.dataset import Dataset
|
||||
from fluents import plots, dataset, workflow, logger
|
||||
from laydi import laydi
|
||||
from laydi.workflow import Function, OptionsDialog, Options
|
||||
from laydi.dataset import Dataset
|
||||
from laydi import plots, dataset, workflow, logger
|
||||
import scipy
|
||||
from engines import pca, pls, nipals_lpls
|
||||
from cx_stats import leverage, variances, hotelling
|
||||
|
|
@ -763,7 +763,7 @@ class PcaOptionsDialog(OptionsDialog):
|
|||
"""
|
||||
def __init__(self, data, options, input_names=['X']):
|
||||
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"
|
||||
page_name = "Options"
|
||||
|
|
@ -975,7 +975,7 @@ class LplsOptionsDialog(OptionsDialog):
|
|||
"""
|
||||
def __init__(self, data, options, input_names=['X', 'Y', 'Z']):
|
||||
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"
|
||||
page_name = "Options"
|
||||
|
|
@ -1179,7 +1179,7 @@ class PlsOptionsDialog(OptionsDialog):
|
|||
"""
|
||||
def __init__(self, data, options, input_names=['X', 'Y']):
|
||||
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"
|
||||
page_name = "Options"
|
||||
|
|
|
|||
|
|
@ -7,8 +7,8 @@ fixme:
|
|||
|
||||
from matplotlib import cm,patches
|
||||
import gtk
|
||||
import fluents
|
||||
from fluents import plots, main,logger
|
||||
import laydi
|
||||
from laydi import plots, main,logger
|
||||
import scipy
|
||||
from scipy import dot,sum,diag,arange,log,mean,newaxis,sqrt,apply_along_axis,empty
|
||||
from scipy.stats import corrcoef
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ import gtk
|
|||
import gobject
|
||||
import plots
|
||||
import time
|
||||
import fluents
|
||||
import laydi
|
||||
from logger import logger
|
||||
import dataset, plots, project, workflow, main
|
||||
import scipy
|
||||
|
|
@ -278,11 +278,11 @@ class NavigatorMenu(gtk.Menu):
|
|||
ds = dataset.read_ftsv(filename)
|
||||
|
||||
if isinstance(ds, dataset.GraphDataset):
|
||||
icon = fluents.icon_factory.get("graph_dataset")
|
||||
icon = laydi.icon_factory.get("graph_dataset")
|
||||
elif isinstance(ds, dataset.CategoryDataset):
|
||||
icon = fluents.icon_factory.get("category_dataset")
|
||||
icon = laydi.icon_factory.get("category_dataset")
|
||||
else:
|
||||
icon = fluents.icon_factory.get("dataset")
|
||||
icon = laydi.icon_factory.get("dataset")
|
||||
|
||||
main.project.add_dataset(ds)
|
||||
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):
|
||||
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)
|
||||
# fixme: image plot selections are not well defined
|
||||
#plot.set_selection_listener(project.set_selection)
|
||||
|
|
@ -342,7 +342,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
def on_plot_hist(self, item, navigator):
|
||||
project = main.project
|
||||
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)
|
||||
plot.set_selection_listener(project.set_selection)
|
||||
project._selection_observers.append(plot)
|
||||
|
|
@ -369,7 +369,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
ids_major[0], ids_major[1],
|
||||
name='Scatter (%s)' % ds_major.get_name())
|
||||
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)
|
||||
plot.set_selection_listener(project.set_selection)
|
||||
project._selection_observers.append(plot)
|
||||
|
|
@ -380,7 +380,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
dims = ds.get_dim_name()
|
||||
ids = ds.get_identifiers(dims[1])
|
||||
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)
|
||||
plot.set_selection_listener(project.set_selection)
|
||||
project._selection_observers.append(plot)
|
||||
|
|
@ -389,7 +389,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
project = main.project
|
||||
ds = self.dataset.transpose()
|
||||
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)
|
||||
|
||||
def on_standardise_rows(self, item, navigator):
|
||||
|
|
@ -398,7 +398,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
ds._name = self.dataset._name + ".rsc"
|
||||
axis = 1
|
||||
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)
|
||||
|
||||
def on_standardise_cols(self, item, navigator):
|
||||
|
|
@ -407,7 +407,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
ds._name = self.dataset._name + ".csc"
|
||||
axis = 0
|
||||
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)
|
||||
|
||||
def on_log(self, item, navigator):
|
||||
|
|
@ -421,7 +421,7 @@ class NavigatorMenu(gtk.Menu):
|
|||
|
||||
ds = self.dataset.copy()
|
||||
ds._array = scipy.log(ds.asarray())
|
||||
icon = fluents.icon_factory.get(ds)
|
||||
icon = laydi.icon_factory.get(ds)
|
||||
ds._name = ds._name + ".log"
|
||||
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_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, 'Unselected', unsel_ds, None, "black", icon)
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ import networkx
|
|||
import scipy
|
||||
from numpy import matlib
|
||||
|
||||
import fluents
|
||||
import laydi
|
||||
import logger
|
||||
import view
|
||||
|
||||
|
|
@ -513,11 +513,11 @@ class ScatterPlot(Plot):
|
|||
def is_mappable_with(self, obj):
|
||||
"""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():
|
||||
return True
|
||||
|
||||
elif isinstance(obj, fluents.dataset.Selection):
|
||||
elif isinstance(obj, laydi.dataset.Selection):
|
||||
if self.current_dim in obj.get_dim_name():
|
||||
return True
|
||||
|
||||
|
|
@ -537,7 +537,7 @@ class ScatterPlot(Plot):
|
|||
# is dataset a vector or matrix?
|
||||
if not n==1:
|
||||
# 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)
|
||||
else:
|
||||
vec = array.sum(1)
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ import os
|
|||
import scipy
|
||||
import gobject
|
||||
import gtk
|
||||
import fluents
|
||||
import laydi
|
||||
import logger, dataset, plots, main
|
||||
|
||||
class Project:
|
||||
|
|
@ -83,7 +83,7 @@ class Project:
|
|||
parent_iter = None
|
||||
|
||||
# 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)
|
||||
|
||||
# Add all returned datasets/plots/selections
|
||||
|
|
@ -91,18 +91,18 @@ class Project:
|
|||
# Any kind of dataset
|
||||
if isinstance(d, dataset.Dataset):
|
||||
if isinstance(d, dataset.GraphDataset):
|
||||
icon = fluents.icon_factory.get("graph_dataset")
|
||||
icon = laydi.icon_factory.get("graph_dataset")
|
||||
elif isinstance(d, dataset.CategoryDataset):
|
||||
icon = fluents.icon_factory.get("category_dataset")
|
||||
icon = laydi.icon_factory.get("category_dataset")
|
||||
else:
|
||||
icon = fluents.icon_factory.get("dataset")
|
||||
icon = laydi.icon_factory.get("dataset")
|
||||
|
||||
self.add_dataset(d)
|
||||
self.data_tree_insert(it, d.get_name(), d, None, "black", icon)
|
||||
|
||||
# Any kind of 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)
|
||||
d.set_selection_listener(self.set_selection)
|
||||
self._selection_observers.append(d)
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ import gtk
|
|||
from matplotlib.patches import Polygon,Rectangle
|
||||
from matplotlib.lines import Line2D
|
||||
|
||||
import fluents
|
||||
import laydi
|
||||
import logger
|
||||
|
||||
|
||||
|
|
@ -212,12 +212,12 @@ class ViewFrame (gtk.Frame):
|
|||
self.set_view(obj)
|
||||
self.focus()
|
||||
|
||||
elif isinstance(obj, fluents.dataset.Dataset):
|
||||
elif isinstance(obj, laydi.dataset.Dataset):
|
||||
view = self.get_view()
|
||||
if view != None and view.is_mappable_with(obj):
|
||||
view._update_color_from_dataset(obj)
|
||||
|
||||
elif isinstance(obj, fluents.dataset.Selection):
|
||||
elif isinstance(obj, laydi.dataset.Selection):
|
||||
view = self.get_view()
|
||||
if view.is_mappable_with(obj):
|
||||
view.selection_changed(self.current_dim, obj)
|
||||
|
|
@ -225,7 +225,7 @@ class ViewFrame (gtk.Frame):
|
|||
|
||||
|
||||
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
|
||||
gtk.Table that holds all the visible Views, and a single ViewFrame
|
||||
|
|
@ -416,7 +416,7 @@ class MainView (gtk.Notebook):
|
|||
|
||||
class View (gtk.Frame):
|
||||
"""The base class of everything that is shown in the center view of
|
||||
fluents.
|
||||
laydi.
|
||||
|
||||
Most views should rather subclass Plot, which automatically handles
|
||||
freezing, creates a toolbar, and sets up matplotlib Figure and Canvas
|
||||
|
|
@ -467,7 +467,7 @@ class PlotMode:
|
|||
def get_icon(self):
|
||||
"""Returns the icon for the PlotMode"""
|
||||
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
|
||||
|
||||
def activate(self):
|
||||
|
|
@ -764,7 +764,7 @@ class PlotToolbar(gtk.Toolbar):
|
|||
btn = gtk.ToggleToolButton()
|
||||
|
||||
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.connect('toggled', self._on_freeze_toggle)
|
||||
|
|
@ -850,7 +850,7 @@ class PlotToolbar(gtk.Toolbar):
|
|||
dialog = gtk.FileChooserDialog('Save plot')
|
||||
dialog.set_action(gtk.FILE_CHOOSER_ACTION_SAVE)
|
||||
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)
|
||||
retval = dialog.run()
|
||||
if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]:
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@ import sys
|
|||
import os
|
||||
import inspect
|
||||
import logger
|
||||
import fluents
|
||||
import laydi
|
||||
import main
|
||||
|
||||
def _workflow_classes(dir, modname):
|
||||
|
|
@ -272,12 +272,12 @@ class OptionsDialog(gtk.Dialog):
|
|||
plot_treeview = gtk.TreeView(plot_list)
|
||||
|
||||
# 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']:
|
||||
plot_list.append((name, use, plot_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.set_property('pixbuf', plot_icon)
|
||||
|
||||
|
|
@ -302,7 +302,7 @@ class OptionsDialog(gtk.Dialog):
|
|||
dataset_treeview = gtk.TreeView(dataset_list)
|
||||
|
||||
# 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']:
|
||||
dataset_list.append((name, use, data_icon))
|
||||
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
#!/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.
|
||||
|
||||
export PYTHONPATH=$PYTHONPATH:.:./workflows
|
||||
./bin/fluents $@
|
||||
./bin/laydi $@
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
|
||||
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
|
||||
analysis with gene ontology background information).
|
||||
|
||||
|
|
|
|||
|
|
@ -52,7 +52,7 @@ def parse_options():
|
|||
help="Output annotations in the cellular component tree.",
|
||||
action="store_true", default=False)
|
||||
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",
|
||||
help="Output annotations in the molecular function tree.",
|
||||
action="store_true", default=False)
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
import os, sys
|
||||
import getopt
|
||||
sys.path.append('../..')
|
||||
from fluents import dataset
|
||||
from laydi import dataset
|
||||
import numpy
|
||||
|
||||
max_val = numpy.inf
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ import matplotlib
|
|||
from scipy import *
|
||||
from scipy.linalg import inv,norm
|
||||
|
||||
sys.path.append("../../fluents/lib")
|
||||
sys.path.append("../../laydi/lib")
|
||||
import select_generators
|
||||
|
||||
def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], scale='scores', verbose=True):
|
||||
|
|
|
|||
|
|
@ -6,9 +6,9 @@ from scipy.linalg import norm
|
|||
from lpls import correlation_loadings
|
||||
|
||||
import rpy_go
|
||||
sys.path.append("../../fluents") # home of dataset
|
||||
sys.path.append("../../fluents/lib") # home of cx_stats
|
||||
sys.path.append("/home/flatberg/fluents/scripts/lpls")
|
||||
sys.path.append("../../laydi") # home of dataset
|
||||
sys.path.append("../../laydi/lib") # home of cx_stats
|
||||
sys.path.append("/home/flatberg/laydi/scripts/lpls")
|
||||
sys.path.append("/home/flatberg/pyblm/")
|
||||
import dataset
|
||||
import cx_stats
|
||||
|
|
|
|||
8
setup.py
8
setup.py
|
|
@ -21,15 +21,15 @@ Programming Language :: Python
|
|||
Topic :: Scientific/Engineering
|
||||
"""
|
||||
|
||||
from fluents.fluents import VERSION
|
||||
from laydi.laydi import VERSION
|
||||
|
||||
def configuration(parent_package='', top_path=None):
|
||||
from numpy.distutils.misc_util import Configuration
|
||||
config = Configuration('', parent_package, top_path)
|
||||
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_subpackage('fluents')
|
||||
config.add_subpackage('laydi')
|
||||
return config
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
|
@ -39,7 +39,7 @@ if __name__ == "__main__":
|
|||
config['author_email'] = 'einarr@pvv.org'
|
||||
# config['short_description'] = short_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['license'] = 'GPL'
|
||||
config['platforms'] = ['Linux']
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
import unittest
|
||||
import sys
|
||||
sys.path.append('../../')
|
||||
from fluents import annotations
|
||||
from laydi import annotations
|
||||
|
||||
class AnnotationsTest(unittest.TestCase):
|
||||
|
||||
|
|
|
|||
|
|
@ -6,8 +6,8 @@ import cPickle
|
|||
import scipy
|
||||
import networkx as nx
|
||||
|
||||
from fluents import logger,plots,workflow,dataset,main
|
||||
from fluents.lib import blmfuncs,nx_utils,cx_utils
|
||||
from laydi import logger,plots,workflow,dataset,main
|
||||
from laydi.lib import blmfuncs,nx_utils,cx_utils
|
||||
|
||||
import gobrowser
|
||||
|
||||
|
|
@ -363,7 +363,7 @@ class MapGene2GO(workflow.Function):
|
|||
workflow.Function.__init__(self, 'gene2go', 'gene->GO')
|
||||
# load data at init
|
||||
try:
|
||||
fname = "/home/flatberg/fluents/data/gene2go.pcl"
|
||||
fname = "/home/flatberg/laydi/data/gene2go.pcl"
|
||||
self._gene2go = cPickle.load(open(fname))
|
||||
except:
|
||||
logger.log("notice", "could not load mapping")
|
||||
|
|
@ -395,7 +395,7 @@ class MapGO2Gene(workflow.Function):
|
|||
workflow.Function.__init__(self, 'go2gene', 'GO->gene')
|
||||
# load data at init
|
||||
try:
|
||||
fname = "/home/flatberg/fluents/data/go2gene.pcl"
|
||||
fname = "/home/flatberg/laydi/data/go2gene.pcl"
|
||||
self._go2gene = cPickle.load(open(fname))
|
||||
except:
|
||||
logger.log("notice", "could not load mapping")
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
import gtk
|
||||
from fluents import dataset, logger, plots, workflow, fluents, project
|
||||
from fluents.lib import blmfuncs
|
||||
from laydi import dataset, logger, plots, workflow, laydi, project
|
||||
from laydi.lib import blmfuncs
|
||||
import geneontology
|
||||
#import gostat
|
||||
from scipy import array, randn, log, ones, zeros
|
||||
|
|
@ -245,7 +245,7 @@ class LoadGOFunction(workflow.Function):
|
|||
browser = GeneOntologyTree(go)
|
||||
label = gtk.Label('_Gene Ontology')
|
||||
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):
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
|
||||
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
|
||||
from matplotlib.nxutils import points_inside_poly
|
||||
import matplotlib
|
||||
|
|
@ -243,7 +243,7 @@ class LoadGOFunction(workflow.Function):
|
|||
browser = GeneOntologyTree(go)
|
||||
label = gtk.Label('_Gene Ontology')
|
||||
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):
|
||||
|
||||
|
|
@ -699,7 +699,7 @@ class DagPlot(plots.Plot):
|
|||
def is_mappable_with(self, obj):
|
||||
"""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():
|
||||
return True
|
||||
return False
|
||||
|
|
@ -718,7 +718,7 @@ class DagPlot(plots.Plot):
|
|||
# is dataset a vector or matrix?
|
||||
if not n==1:
|
||||
# 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)
|
||||
else:
|
||||
vec = array.sum(1)
|
||||
|
|
|
|||
|
|
@ -3,8 +3,8 @@ import os.path
|
|||
import webbrowser
|
||||
import cPickle
|
||||
|
||||
from fluents import logger, plots,workflow,dataset,main
|
||||
from fluents.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
|
||||
from laydi import logger, plots,workflow,dataset,main
|
||||
from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
|
||||
import gobrowser, geneontology
|
||||
import scipy
|
||||
import networkx as nx
|
||||
|
|
@ -103,7 +103,7 @@ class DatasetLoadFunctionCYCLE(workflow.Function):
|
|||
workflow.Function.__init__(self, 'load_data', 'Cycle')
|
||||
|
||||
def run(self):
|
||||
filename='fluents/data/CYCLE'
|
||||
filename='laydi/data/CYCLE'
|
||||
if filename:
|
||||
return dataset.from_file(filename)
|
||||
|
||||
|
|
@ -419,7 +419,7 @@ class MapGene2GO(workflow.Function):
|
|||
workflow.Function.__init__(self, 'gene2go', 'gene->GO')
|
||||
# load data at init
|
||||
try:
|
||||
fname = "/home/flatberg/fluents/data/gene2go.pcl"
|
||||
fname = "/home/flatberg/laydi/data/gene2go.pcl"
|
||||
self._gene2go = cPickle.load(open(fname))
|
||||
except:
|
||||
logger.log("notice", "could not load mapping")
|
||||
|
|
@ -451,7 +451,7 @@ class MapGO2Gene(workflow.Function):
|
|||
workflow.Function.__init__(self, 'go2gene', 'GO->gene')
|
||||
# load data at init
|
||||
try:
|
||||
fname = "/home/flatberg/fluents/data/go2gene.pcl"
|
||||
fname = "/home/flatberg/laydi/data/go2gene.pcl"
|
||||
self._go2gene = cPickle.load(open(fname))
|
||||
except:
|
||||
logger.log("notice", "could not load mapping")
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
import gtk
|
||||
from fluents import dataset, logger, plots, workflow
|
||||
from laydi import dataset, logger, plots, workflow
|
||||
#import geneontology
|
||||
#import gostat
|
||||
from scipy import array, randn, log, ones
|
||||
|
|
|
|||
Reference in New Issue