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fixes

This commit is contained in:
Arnar Flatberg 2006-08-28 12:06:05 +00:00
parent 7eb3fa8b46
commit 97e652edce
7 changed files with 91 additions and 50 deletions
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21
system/dataset.py
View File

@ -57,8 +57,8 @@ class Dataset:
else: else:
raise ValueError, "Array input must be of ArrayType" raise ValueError, "Array input must be of ArrayType"
def __str__(self): #def __str__(self):
return self._name + ":\n" + "Dim names: " + self._dims.__str__() # return self._name + ":\n" + "Dim names: " + self._dims.__str__()
def __iter__(self): def __iter__(self):
"""Returns an iterator over dimensions of dataset.""" """Returns an iterator over dimensions of dataset."""
@ -181,7 +181,7 @@ class Dataset:
if idents==None: if idents==None:
index = array_sort(self._map[dim].values()) index = array_sort(self._map[dim].values())
else: else:
index = [self._map[dim][key] for key in idents] index = [self._map[dim][key] for key in idents if self._map[dim].has_key(key)]
return asarray(index) return asarray(index)
class CategoryDataset(Dataset): class CategoryDataset(Dataset):
@ -236,7 +236,7 @@ class GraphDataset(Dataset):
def asnetworkx(self,nx_type='graph'): def asnetworkx(self,nx_type='graph'):
dim = self.get_dim_name()[0] dim = self.get_dim_name()[0]
ids = self.get_identifiers(dim) ids = self.get_identifiers(dim,sorted=True)
adj_mat = self.asarray() adj_mat = self.asarray()
G = self._graph_from_adj_matrix(adj_mat,labels=ids) G = self._graph_from_adj_matrix(adj_mat,labels=ids)
self.has_graph = True self.has_graph = True
@ -271,11 +271,6 @@ class GraphDataset(Dataset):
return G return G
Dataset._all_dims=set() Dataset._all_dims=set()
class Selection:
"""Handles selected identifiers along each dimension of a dataset"""
def __init__(self):
self.current_selection={}
class ReverseDict(dict): class ReverseDict(dict):
""" """
@ -300,7 +295,7 @@ def to_file(filepath,dataset,name=None):
""" """
if not name: if not name:
name = dataset._name name = dataset._name
data = shelve.open(filepath,protocol=2) data = shelve.open(filepath,flag='c',protocol=2)
if data: #we have an append if data: #we have an append
names = data.keys() names = data.keys()
if name in names: if name in names:
@ -311,7 +306,7 @@ def to_file(filepath,dataset,name=None):
def from_file(filepath): def from_file(filepath):
"""Read dataset from file """ """Read dataset from file """
data = shelve.open(filepath) data = shelve.open(filepath,flag='r')
out_data = [] out_data = []
for name in data.keys(): for name in data.keys():
sub_data = data[name] sub_data = data[name]
@ -324,3 +319,7 @@ def from_file(filepath):
return out_data return out_data
class Selection:
"""Handles selected identifiers along each dimension of a dataset"""
def __init__(self):
self.current_selection={}

2
system/fluents.py
View File

@ -80,6 +80,8 @@ class FluentApp:
self.init_gui() self.init_gui()
def change_plot(self, plot): def change_plot(self, plot):
# add current selection to new plot
plot.selection_changed(self.project.get_selection())
pt = self.widget_tree.get_widget('main_view') pt = self.widget_tree.get_widget('main_view')
pt.insert_view(plot) pt.insert_view(plot)

26
system/navigator.py
View File

@ -18,7 +18,6 @@ class NavigatorView (gtk.TreeView):
# various properties # various properties
self.set_headers_visible(False) self.set_headers_visible(False)
# Selection Mode # Selection Mode
self.get_selection().set_mode(gtk.SELECTION_MULTIPLE) self.get_selection().set_mode(gtk.SELECTION_MULTIPLE)
self.get_selection().set_select_function(self.is_selectable) self.get_selection().set_select_function(self.is_selectable)
@ -29,11 +28,11 @@ class NavigatorView (gtk.TreeView):
# self.connect('cursor_changed', self.cursor_changed_handler) # self.connect('cursor_changed', self.cursor_changed_handler)
self.connect('row_activated', self.row_activated_handler) self.connect('row_activated', self.row_activated_handler)
textrenderer = gtk.CellRendererText() self.textrenderer = textrenderer = gtk.CellRendererText()
textrenderer.set_property('foreground_set',True)
self.object_col = gtk.TreeViewColumn('Object') self.object_col = gtk.TreeViewColumn('Object')
self.object_col.pack_start(textrenderer) self.object_col.pack_start(textrenderer,expand=False)
self.object_col.set_attributes(textrenderer, cell_background=3, foreground = 4, text=0) self.object_col.set_attributes(textrenderer, cell_background=3, foreground=4, text=0)
self.append_column(self.object_col) self.append_column(self.object_col)
# send events to plots / itself # send events to plots / itself
@ -46,12 +45,11 @@ class NavigatorView (gtk.TreeView):
# sets data for drag event. # sets data for drag event.
def slot_drag_data(self,treeview,context,selection,target_id,etime): def slot_drag_data(self,treeview,context,selection,target_id,etime):
treeselection = treeview.get_selection() treeselection = treeview.get_selection()
model, paths = treeselection.get_selected_rows() model, paths = treeselection.get_selected_rows()
if paths: if paths:
self.data_tree.drag_data_get(paths[0], selection) self.data_tree.drag_data_get(paths[0], selection)
def add_project(self, project): def add_project(self, project):
self.project = project self.project = project
self.data_tree = project.data_tree self.data_tree = project.data_tree
@ -69,12 +67,13 @@ class NavigatorView (gtk.TreeView):
# selection changed, setting current_data ojbects # selection changed, setting current_data ojbects
def selection_changed_handler(self, selection): def selection_changed_handler(self, selection):
# update prev selection right away in case of multiple events # update prev selection right away in case of multiple events
model, paths = selection.get_selected_rows() model, paths = selection.get_selected_rows()
tmp = self._previous_selection if not paths: # a plot is marked: do nothing
return
tmp = self._previous_selection
self._previous_selection = paths self._previous_selection = paths
# set timestamp on newly selected objects # set timestamp on newly selected objects
[self.data_tree.set_value(self.data_tree.get_iter(path),5,time.time()) for path in paths if path not in tmp] [self.data_tree.set_value(self.data_tree.get_iter(path),5,time.time()) for path in paths if path not in tmp]
@ -99,7 +98,6 @@ class NavigatorView (gtk.TreeView):
if not (treestore.get_value(iter,2) or treestore.get_value(iter,1)): if not (treestore.get_value(iter,2) or treestore.get_value(iter,1)):
return return
self.expand_to_path(pos) self.expand_to_path(pos)
if isinstance(obj,dataset.Dataset): if isinstance(obj,dataset.Dataset):
@ -121,7 +119,7 @@ class NavigatorView (gtk.TreeView):
d.set_default_response(gtk.BUTTONS_OK) d.set_default_response(gtk.BUTTONS_OK)
d.run() d.run()
d.destroy() d.destroy()
def row_activated_handler(self, widget, path, column): def row_activated_handler(self, widget, path, column):
tree_iter = self.data_tree.get_iter(path) tree_iter = self.data_tree.get_iter(path)
obj = self.data_tree.get_value(tree_iter, 2) obj = self.data_tree.get_value(tree_iter, 2)

68
system/plots.py
View File

@ -238,6 +238,7 @@ class Plot (gtk.Frame):
self.fig = Figure(figsize=(5,4), dpi=72) self.fig = Figure(figsize=(5,4), dpi=72)
self.canvas = FigureCanvas(self.fig) self.canvas = FigureCanvas(self.fig)
self.fig.set_facecolor('white') self.fig.set_facecolor('white')
def get_title(self): def get_title(self):
return self.title return self.title
@ -394,6 +395,8 @@ class LineViewPlot(Plot):
ps: slow (cant get linecollection and blit to work) ps: slow (cant get linecollection and blit to work)
""" """
def __init__(self, dataset,major_axis=1,minor_axis=None, name="Line view"): def __init__(self, dataset,major_axis=1,minor_axis=None, name="Line view"):
self.use_blit = False
self._last_index = []
self._data = dataset.asarray() self._data = dataset.asarray()
self.dataset = dataset self.dataset = dataset
Plot.__init__(self, name) Plot.__init__(self, name)
@ -407,7 +410,10 @@ class LineViewPlot(Plot):
x_axis = scipy.arrayrange(self._data.shape[minor_axis]) x_axis = scipy.arrayrange(self._data.shape[minor_axis])
for i in range(self._data.shape[major_axis]): for i in range(self._data.shape[major_axis]):
yi = scipy.take(self._data,[i],axis=major_axis) yi = scipy.take(self._data,[i],axis=major_axis)
l, = self.ax.plot(x_axis,yi,'k',alpha=.05,animated=True) if self.use_blit:
l,=self.ax.plot(x_axis,yi,'k',alpha=.05,animated=True)
else:
l,=self.ax.plot(x_axis,yi,'k',alpha=.05)
self.line_collection[i] = l self.line_collection[i] = l
self.add(self.canvas) self.add(self.canvas)
@ -427,18 +433,33 @@ class LineViewPlot(Plot):
def selection_changed(self, selection): def selection_changed(self, selection):
ids = selection[self.current_dim] # current identifiers ids = selection[self.current_dim] # current identifiers
index = self.dataset.get_indices(self.current_dim, ids) index = self.dataset.get_indices(self.current_dim, ids)
if self._background is None: if self.use_blit:
print "background needs copy" if self._background is None:
self._background = self.canvas.copy_from_bbox(self.ax.bbox) self._last_index = None
print self.ax.bbox.get_bounds() self._background = self.canvas.copy_from_bbox(self.ax.bbox)
self.canvas.restore_region(self._background)
self.canvas.restore_region(self._background)
if index: if index:
if self._last_index:
for i in self._last_index:
# if not using blit: reset last selection
self.ax.lines[i].set_color('k')
self.ax.lines[i].set_alpha(.05)
self.ax.lines[i].set_zorder(1)
for i in index: for i in index:
self.line_collection[i].set_visible(True) self.ax.lines[i].set_color('r')
self.line_collection[i].set_color('r') self.ax.lines[i].set_alpha(1.0)
self.line_collection[i].set_alpha(1.0) self.ax.lines[i].set_visible(True)
self.ax.draw_artist(self.line_collection[i]) self.ax.lines[i].set_zorder(3)
self.canvas.blit() if self.use_blit:
self.ax.draw_artist(self.ax.lines[i])
#else:
# self.ax.add_line(self.line_collection[i])
self._last_index = index
if self.use_blit:
self.canvas.blit()
else:
self.canvas.draw()
class ScatterMarkerPlot(Plot): class ScatterMarkerPlot(Plot):
"""The ScatterMarkerPlot is faster than regular scatterplot, but """The ScatterMarkerPlot is faster than regular scatterplot, but
@ -446,9 +467,14 @@ has no color and size options."""
def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2, name="Scatter plot"): def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2, name="Scatter plot"):
Plot.__init__(self, name) Plot.__init__(self, name)
self.ax = ax = self.fig.add_subplot(111) self.ax = ax = self.fig.add_subplot(111)
#self.ax.set_position([0.01,0.01,.99,.99])
self.ax.set_xticks([])
self.ax.set_yticks([])
self.ax.axhline(0,color='k',lw=1.5,zorder=0)
self.ax.axvline(0,color='k',lw=1.5,zorder=0)
self.current_dim = id_dim self.current_dim = id_dim
self.dataset_1 = dataset_1 self.dataset_1 = dataset_1
self._selection_line = None
x_index = dataset_1[sel_dim][id_1] x_index = dataset_1[sel_dim][id_1]
y_index = dataset_2[sel_dim][id_2] y_index = dataset_2[sel_dim][id_2]
@ -493,9 +519,9 @@ has no color and size options."""
xdata_new = scipy.take(self.xaxis_data, index) #take data xdata_new = scipy.take(self.xaxis_data, index) #take data
ydata_new = scipy.take(self.yaxis_data, index) ydata_new = scipy.take(self.yaxis_data, index)
#remove old selection #remove old selection
if len(self.ax.lines)>1: if self._selection_line:
del self.ax.lines[-1] self.ax.lines.remove(self._selection_line)
self.ax.plot(xdata_new,ydata_new,'ok') self._selection_line, = self.ax.plot(xdata_new,ydata_new,'or')
self._toolbar.forward() #update data lims before draw self._toolbar.forward() #update data lims before draw
self.canvas.draw() self.canvas.draw()
@ -505,6 +531,7 @@ has no color and size options."""
def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,c='b',s=30, name="Scatter plot"): def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,c='b',s=30, name="Scatter plot"):
Plot.__init__(self, name) Plot.__init__(self, name)
self.ax = ax = self.fig.add_subplot(111) self.ax = ax = self.fig.add_subplot(111)
#self.ax.set_position([0.01,0.01,.99,.99])
self.current_dim = id_dim self.current_dim = id_dim
self.dataset_1 = dataset_1 self.dataset_1 = dataset_1
@ -516,8 +543,8 @@ has no color and size options."""
ax.scatter(self.xaxis_data,self.yaxis_data,s=s,c=c,faceted=False,edgecolor='k') ax.scatter(self.xaxis_data,self.yaxis_data,s=s,c=c,faceted=False,edgecolor='k')
ax.set_title(self.get_title()) ax.set_title(self.get_title())
ax.set_xlabel("%s - %s" % (sel_dim, id_1)) #ax.set_xlabel("%s - %s" % (sel_dim, id_1))
ax.set_ylabel("%s - %s" % (sel_dim, id_2)) #ax.set_ylabel("%s - %s" % (sel_dim, id_2))
# collection # collection
self.coll = ax.collections[0] self.coll = ax.collections[0]
@ -553,8 +580,10 @@ has no color and size options."""
ids = selection[self.current_dim] # current identifiers ids = selection[self.current_dim] # current identifiers
index = self.dataset_1.get_indices(self.current_dim, ids) index = self.dataset_1.get_indices(self.current_dim, ids)
lw = scipy.zeros(self.xaxis_data.shape,'f') lw = scipy.zeros(self.xaxis_data.shape,'f')
zo = lw.copy() + 1 #z-order
scipy.put(lw,index,2.) scipy.put(lw,index,2.)
self.coll.set_linewidth(lw) self.coll.set_linewidth(lw)
self.coll.set_zorder(zo)
self._toolbar.forward() #update data lims before draw self._toolbar.forward() #update data lims before draw
self.canvas.draw() self.canvas.draw()
@ -598,6 +627,9 @@ class NetworkPlot(Plot):
kw.pop('node_color') kw.pop('node_color')
self.ax = self.fig.add_subplot(111) self.ax = self.fig.add_subplot(111)
self.ax.set_position([0.01,0.01,.99,.99])
self.ax.set_xticks([])
self.ax.set_yticks([])
# FIXME: ax shouldn't be in kw at all # FIXME: ax shouldn't be in kw at all
if kw.has_key('ax'): if kw.has_key('ax'):
kw.pop('ax') kw.pop('ax')
@ -659,7 +691,7 @@ class NetworkPlot(Plot):
self.ax.clear() self.ax.clear()
networkx.draw_networkx_edges(self.graph, edge_list=self.graph.edges(), \ networkx.draw_networkx_edges(self.graph, edge_list=self.graph.edges(), \
ax=self.ax, **self.keywords) ax=self.ax, **self.keywords)
networkx.draw_networkx_labels(self.graph,**self.keywords)
if unselected_nodes: if unselected_nodes:
networkx.draw_networkx_nodes(self.graph, nodelist=unselected_nodes, \ networkx.draw_networkx_nodes(self.graph, nodelist=unselected_nodes, \
node_color='r', node_size=unselected_sizes, ax=self.ax, **self.keywords) node_color='r', node_size=unselected_sizes, ax=self.ax, **self.keywords)

14
system/project.py
View File

@ -2,6 +2,7 @@
import scipy import scipy
import gobject import gobject
import gtk import gtk
import logger
from system import dataset, plots from system import dataset, plots
class Project: class Project:
@ -70,11 +71,17 @@ class Project:
it = self.data_tree_insert(parent_iter, fun, None, "grey","black") it = self.data_tree_insert(parent_iter, fun, None, "grey","black")
for d in data: for d in data:
if isinstance(d, dataset.Dataset): if isinstance(d, dataset.GraphDataset):
self.add_dataset(d) self.add_dataset(d)
self.data_tree_insert(it, d.get_name(), d, "white", "blue") self.data_tree_insert(it, d.get_name(), d, "LightPink", "black")
elif isinstance(d,dataset.CategoryDataset):
self.add_dataset(d)
self.data_tree_insert(it, d.get_name(), d, "LightSalmon", "black")
elif isinstance(d, dataset.Dataset):
self.add_dataset(d)
self.data_tree_insert(it, d.get_name(), d, "LightSkyBlue", "black")
elif isinstance(d, plots.Plot): elif isinstance(d, plots.Plot):
self.data_tree_insert(it, d.get_title(), d, "white", "dark green") self.data_tree_insert(it, d.get_title(), d, "PaleGreen", "black")
d.set_selection_listener(self.set_selection) d.set_selection_listener(self.set_selection)
self._selection_observers.append(d) self._selection_observers.append(d)
@ -91,6 +98,7 @@ class Project:
def add_dataset(self,dataset): def add_dataset(self,dataset):
"""Appends a new Dataset to the project.""" """Appends a new Dataset to the project."""
logger.log('debug','Adding dataset: %s' %dataset.get_name())
self.datasets.append(dataset) self.datasets.append(dataset)
for dim_name in dataset.get_all_dims(): for dim_name in dataset.get_all_dims():
if dim_name not in self.dim_names: if dim_name not in self.dim_names:

2
system/workflow.py
View File

@ -41,7 +41,7 @@ def workflow_list():
except Exception, e: except Exception, e:
logger.log('warning', 'Cannot load workflow: %s' % fn) logger.log('warning', 'Cannot load workflow: %s' % fn)
logger.log('warning', e) logger.log('warning', e)
return retval return retval
class Workflow: class Workflow:

8
workflows/pca_workflow.py
View File

@ -6,6 +6,8 @@ from scipy import log2,transpose,dot,divide,shape,mean,resize,zeros
from scipy.linalg import svd,inv,norm,get_blas_funcs,eig from scipy.linalg import svd,inv,norm,get_blas_funcs,eig
from system import dataset, logger, plots from system import dataset, logger, plots
class PCAWorkflow(wf.Workflow): class PCAWorkflow(wf.Workflow):
name = 'PCA Workflow' name = 'PCA Workflow'
ident = 'pca' ident = 'pca'
@ -96,9 +98,9 @@ class PCAFunction(Function):
row_ids = data.get_identifiers('genes') row_ids = data.get_identifiers('genes')
col_ids = data.get_identifiers('samples') col_ids = data.get_identifiers('samples')
T = dataset.Dataset(T,[('samples',col_ids) ,comp_def]) T = dataset.Dataset(T,[('samples',col_ids) ,comp_def],name='T2')
P = dataset.Dataset(P,[('genes',row_ids),comp_def]) P = dataset.Dataset(P,[('genes',row_ids),comp_def],name='P')
E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)]) E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)],name='E')
#tsq = dataset.Dataset(tsq,[singel_def,data_ids[1]) #tsq = dataset.Dataset(tsq,[singel_def,data_ids[1])
## plots ## plots