Projects/laydi
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The navigator now displays the plots and data in a tree that shows the ancestry information.

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This commit is contained in:
Einar Ryeng 2006-04-24 14:52:21 +00:00
parent 6c72dec7fa
commit 179a2f88a9
6 changed files with 80 additions and 44 deletions
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1
fluent
View File

@ -53,6 +53,7 @@ class FluentApp:
def create_logview(self, str1, str2, int1, int2):
# Set up log view
self.log_view = logger.LogView(logger.logger)
self.log_view.set_level('notice')
self.log_view.show()
return self.log_view

5
system/logger.py
View File

@ -58,7 +58,10 @@ class LogView(gtk.TreeView):
#self.connect('button_release_event', None)
# Make sure tree view displays bottom entry when entered
self.model.connect('row-changed', lambda model, path, iter : self.scroll_to_cell(path))
def scroll_to_last(model, path, it):
if path:
self.scroll_to_cell(path)
self.model.connect('row-changed', scroll_to_last)
def set_level(self, level):
self.level = level

18
system/plots.py
View File

@ -161,13 +161,17 @@ class LargeView (gtk.Frame):
class Plot (gtk.Frame):
def __init__(self):
def __init__(self, title):
gtk.Frame.__init__(self)
self.mark_active(False)
self.connect('button_press_event', self.on_button_press)
self.sel_obj = None
self.active = False
self.title = title
def get_title(self):
return self.title
def on_button_press(self, *rest):
# logger.log('debug', 'button pressed in plot')
self.mark_active(True)
@ -188,7 +192,7 @@ class Plot (gtk.Frame):
class EmptyView (Plot):
def __init__(self):
Plot.__init__(self)
Plot.__init__(self, 'Empty view')
label = gtk.Label('No view')
ebox = gtk.EventBox()
@ -213,20 +217,22 @@ class EmptyView (Plot):
class SinePlot(Plot):
def __init__(self):
Plot.__init__(self)
Plot.__init__(self, 'Sine plot')
fig = Figure(figsize=(5,4), dpi=72)
ax = fig.add_subplot(111)
t = arange(0.0,3.0,0.01)
s = sin(2*pi*t)
ax.plot(t,s)
self.canvas = FigureCanvas(fig)
self.add(self.canvas)
self.canvas.show()
class ScatterPlot(Plot):
def __init__(self, dataset, id_dim, sel_dim, id_1, id_2):
Plot.__init__(self)
def __init__(self, dataset,id_dim, sel_dim,id_1,id_2):
Plot.__init__(self, 'Scatter plot')
fig = Figure(figsize=(5,4), dpi=72)
self.ax = ax = fig.add_subplot(111)
self.current_dim = id_dim

28
system/project.py
View File

@ -45,28 +45,42 @@ class Project:
def get_selection(self):
"""Returns the current selection object"""
return self.sel_obj.current_selection
def get_data_iter(self, obj):
"""Retuns an iterator to data."""
retval = [None]
def is_obj(m, p, i, d):
if obj == m.get_value(i, 2):
d.append(i)
return True
self.data_tree.foreach(is_obj, retval)
return retval[-1]
def add_data(self, parent, data):
"""Adds a set of data and plots to the navigator.
This method is usually called after a Function in a workflow
has finished and returns its output."""
parent_iter = self.get_data_iter(parent)
for d in data:
if isinstance(d, dataset.Dataset):
self.add_dataset(d)
self.data_tree_insert(None, d.get_name(), d)
self.data_tree_insert(parent_iter, d.get_name(), d)
elif isinstance(d, plots.Plot):
# self.add_view(d)
self.data_tree_insert(None, 'view', d)
self.data_tree_insert(parent_iter, d.get_title(), d)
d.set_project(self)
self.attach(d, 'selection_update')
def data_tree_insert(self, parent, text, data):
tree = self.data_tree
iter = tree.append(parent)
tree.set_value(iter, 0, text)
tree.set_value(iter, 1, type(data))
tree.set_value(iter, 2, data)
it = tree.append(parent)
tree.set_value(it, 0, text)
tree.set_value(it, 1, type(data))
tree.set_value(it, 2, data)
def add_dataset(self,dataset):
"""Appends a new Dataset to the project."""

5
system/workflow.py
View File

@ -116,9 +116,12 @@ class WorkflowView (gtk.VBox):
def run_function(self, function):
logger.log('debug', 'Starting function: %s' % function.name)
project = self.workflow.app.project
parent_data = project.current_data
new_data = function.run(project.current_data)
if new_data != None:
project.add_data(None, new_data)
project.add_data(parent_data, new_data)
logger.log('debug', 'Function ended: %s' % function.name)
def button_click_handler(self, button):

67
workflows/go_workflow.py
View File

@ -1,55 +1,55 @@
import gtk
import logger
from annotations import Annotations
from workflow import *
import workflow
import plots
import dataset
#import geneontology
#import gostat
from scipy import array,randn
from scipy import array,randn,log
import cPickle
class EinarsWorkflow (Workflow):
class EinarsWorkflow (workflow.Workflow):
name = 'Test Workflow'
description = 'Gene Ontology Workflow. This workflow currently serves as a general testing workflow.'
def __init__(self, app):
Workflow.__init__(self, app)
workflow.Workflow.__init__(self, app)
load = Stage('load', 'Load Data')
load.add_function(Function('load', 'Load Microarrays'))
load = workflow.Stage('load', 'Load Data')
load.add_function(CelFileImportFunction())
load.add_function(TestDataFunction())
load.add_function(DatasetLoadFunction())
self.add_stage(load)
preproc = Stage('preprocess', 'Preprocessing')
preproc.add_function(Function('rma', 'RMA'))
preproc = workflow.Stage('preprocess', 'Preprocessing')
preproc.add_function(DatasetLog())
preproc.add_function(workflow.Function('rma', 'RMA'))
self.add_stage(preproc)
go = Stage('go', 'Gene Ontology Data')
go = workflow.Stage('go', 'Gene Ontology Data')
go.add_function(LoadAnnotationsFunction())
go.add_function(GODistanceFunction())
self.add_stage(go)
regression = Stage('regression', 'Regression')
regression.add_function(Function('pls', 'PLS'))
regression = workflow.Stage('regression', 'Regression')
regression.add_function(workflow.Function('pls', 'PLS'))
self.add_stage(regression)
explore = Stage('explore', 'Explorative analysis')
explore = workflow.Stage('explore', 'Explorative analysis')
explore.add_function(PCAFunction(self))
self.add_stage(explore)
save = Stage('save', 'Save Data')
save = workflow.Stage('save', 'Save Data')
save.add_function(DatasetSaveFunction())
self.add_stage(save)
logger.log('debug', '\tEinar\'s workflow is now active')
class LoadAnnotationsFunction(Function):
class LoadAnnotationsFunction(workflow.Function):
def __init__(self):
Function.__init__(self, 'load-go-ann', 'Load Annotations')
workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
self.annotations = None
def load_file(self, filename):
@ -80,10 +80,10 @@ class LoadAnnotationsFunction(Function):
dialog.destroy()
return [self.annotations]
class GODistanceFunction(Function):
class GODistanceFunction(workflow.Function):
def __init__(self):
Function.__init__(self, 'go_diatance', 'GO Distances')
workflow.Function.__init__(self, 'go_diatance', 'GO Distances')
self.output = None
def run(self, data):
@ -99,9 +99,9 @@ class GODistanceFunction(Function):
return gene_distances
class TestDataFunction(Function):
class TestDataFunction(workflow.Function):
def __init__(self):
Function.__init__(self, 'test_data', 'Generate Test Data')
workflow.Function.__init__(self, 'test_data', 'Generate Test Data')
def run(self, data):
logger.log('notice', 'Injecting foo test data')
@ -109,11 +109,20 @@ class TestDataFunction(Function):
X = dataset.Dataset(x)
return [X, plots.SinePlot()]
class DatasetLog(workflow.Function):
def __init__(self):
workflow.Function.__init__(self, 'log', 'Log')
class DatasetLoadFunction(Function):
def run(self, data):
logger.log('notice', 'Taking the log of dataset %s' % data.get_name())
d = data.asarray()
d = log(d)
return [dataset.Dataset(d)]
class DatasetLoadFunction(workflow.Function):
"""Loader for previously pickled Datasets."""
def __init__(self):
Function.__init__(self, 'load_data', 'Load Pickled Dataset')
workflow.Function.__init__(self, 'load_data', 'Load Pickled Dataset')
def run(self, data):
chooser = gtk.FileChooserDialog(title="Select cel files...", parent=None,
@ -136,10 +145,10 @@ class DatasetLoadFunction(Function):
chooser.destroy()
class DatasetSaveFunction(Function):
class DatasetSaveFunction(workflow.Function):
"""QND way to save data to file for later import to this program."""
def __init__(self):
Function.__init__(self, 'save_data', 'Save Pickled Dataset')
workflow.Function.__init__(self, 'save_data', 'Save Pickled Dataset')
def run(self, data):
if not data:
@ -168,10 +177,10 @@ class DatasetSaveFunction(Function):
chooser.destroy()
class CelFileImportFunction(Function):
class CelFileImportFunction(workflow.Function):
"""Loads AffyMetrix .CEL-files into matrix."""
def __init__(self):
Function.__init__(self, 'cel_import', 'Import Affy')
workflow.Function.__init__(self, 'cel_import', 'Import Affy')
def run(self, data):
import rpy
@ -214,11 +223,11 @@ class CelFileImportFunction(Function):
chooser.destroy()
class PCAFunction(Function):
class PCAFunction(workflow.Function):
"""Generic PCA function."""
def __init__(self, workflow):
Function.__init__(self, 'pca', 'PCA')
self._workflow = workflow
def __init__(self, wf):
workflow.Function.__init__(self, 'pca', 'PCA')
self._workflow = wf
def run(self, data):
import rpy