mainly overhaul of observers, and removal of project singleton
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parent
f45c9c6bf7
commit
6a4ae8ecf1
21
fluent
21
fluent
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@ -14,10 +14,12 @@ import gnome.ui
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import pango
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import pango
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import project
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import project
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import workflow
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import workflow
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import dataset
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import logger
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import logger
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import plots
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import plots
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import navigator
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import navigator
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import go_workflow
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import go_workflow
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import scipy
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PROGRAM_NAME = 'fluent'
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PROGRAM_NAME = 'fluent'
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VERSION = '0.1.0'
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VERSION = '0.1.0'
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@ -29,11 +31,22 @@ class FluentApp:
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def __init__(self):
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def __init__(self):
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# Application variables
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# Application variables
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self.navigator = navigator.NavigatorStore()
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self.current_data = None
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self.project = project.Project()
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self.project = project.Project()
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# add test data ##################
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x = scipy.rand(200,3)
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def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
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test_data1 = dataset.Dataset(x,def_list)
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self.project.add_dataset(test_data1)
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#y = scipy.rand(200,2)
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#def_list = [ ['samples',[]], ['yclasses',['C','N']] ]
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#test_data2 = dataset.Dataset(y,def_list)
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####################
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self.navigator = navigator.NavigatorStore(self.project)
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self.current_data = None
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gtk.glade.set_custom_handler(self.custom_object_factory)
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gtk.glade.set_custom_handler(self.custom_object_factory)
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self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
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self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
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self.workflow = go_workflow.EinarsWorkflow(self)
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self.workflow = go_workflow.EinarsWorkflow(self)
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@ -59,7 +72,7 @@ class FluentApp:
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self.small_view.show()
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self.small_view.show()
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return self.small_view
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return self.small_view
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def create_large_view(self, str1, str2, int1, int2):
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def create_large_view(self, str1, str2, int1, int2,project):
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self.large_view = plots.LargeView()
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self.large_view = plots.LargeView()
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self.large_view.show()
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self.large_view.show()
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return self.large_view
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return self.large_view
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@ -22,9 +22,10 @@ class Dataset:
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raise ValueError,"array dims and identifyer mismatch"
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raise ValueError,"array dims and identifyer mismatch"
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for axis,(dim_name,ids) in enumerate(def_list):
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for axis,(dim_name,ids) in enumerate(def_list):
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enum_ids = {}
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enum_ids = {}
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if dim_name not in project.c_p.dim_names:
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#if dim_name not in project.c_p.dim_names:
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dim_name = project.c_p.suggest_dim_name(dim_name)
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# dim_name = project.c_p.suggest_dim_name(dim_name)
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if not ids:
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if not ids:
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logger.log('debug','Creating identifiers along: '+dim_name)
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ids = self._create_identifiers(axis)
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ids = self._create_identifiers(axis)
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for num,name in enumerate(ids):
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for num,name in enumerate(ids):
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enum_ids[name] = num
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enum_ids[name] = num
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@ -70,6 +71,7 @@ class Dataset:
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dim_ids = self.ids[dim_name]
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dim_ids = self.ids[dim_name]
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if type(index)==int:
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if type(index)==int:
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index = [index]
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index = [index]
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return set([id for id,ind in dim_ids.items() if ind in index])
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return set([id for id,ind in dim_ids.items() if ind in index])
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def extract_index_from_id(self,dim_name,id):
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def extract_index_from_id(self,dim_name,id):
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@ -5,22 +5,20 @@ import plots
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import logger
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import logger
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class NavigatorStore (gtk.TreeStore):
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class NavigatorStore (gtk.TreeStore):
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def __init__(self):
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def __init__(self,project):
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gtk.TreeStore.__init__(self, gobject.TYPE_STRING, plots.Plot)
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gtk.TreeStore.__init__(self, gobject.TYPE_STRING, plots.Plot)
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self.project = project
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iter = self.append(None)
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iter = self.append(None)
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self.set_value(iter, 0, ('Sine Plot'))
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self.set_value(iter, 0, ('Sine Plot'))
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self.set_value(iter, 1, (plots.SinePlot()))
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self.set_value(iter, 1, (plots.SinePlot(project)))
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iter = self.append(None)
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iter = self.append(None)
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self.set_value(iter, 0, ('Scatter Plot'))
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self.set_value(iter, 0, ('Scatter Plot'))
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self.set_value(iter, 1, (plots.ScatterPlot()))
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self.set_value(iter, 1, (plots.ScatterPlot(project)))
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iter = self.append(None)
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iter = self.append(None)
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self.set_value(iter, 0, ('Scatter Plot 2'))
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self.set_value(iter, 0, ('Scatter Plot 2'))
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self.set_value(iter, 1, (plots.ScatterPlot()))
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self.set_value(iter, 1, (plots.ScatterPlot(project)))
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def plot_at(self, path):
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def plot_at(self, path):
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iter = self.get_iter(path)
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iter = self.get_iter(path)
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@ -163,12 +163,14 @@ class LargeView (gtk.Frame):
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class Plot (gtk.Frame):
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class Plot (gtk.Frame):
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def __init__(self):
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def __init__(self,project):
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gtk.Frame.__init__(self)
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gtk.Frame.__init__(self)
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self.project = project
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self.mark_active(False)
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self.mark_active(False)
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self.connect('button_press_event', self.on_button_press)
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self.connect('button_press_event', self.on_button_press)
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self.sel_obj = None
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self.sel_obj = None
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project.c_p.attach(self)
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if project!=None: #its not an Emptyview
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project.attach(self,'selection_update')
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def on_button_press(self, *rest):
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def on_button_press(self, *rest):
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logger.log('debug', 'button pressed in plot')
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logger.log('debug', 'button pressed in plot')
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@ -183,12 +185,12 @@ class Plot (gtk.Frame):
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else:
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else:
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self.set_shadow_type(gtk.SHADOW_OUT)
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self.set_shadow_type(gtk.SHADOW_OUT)
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def update_selection(self,project):
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def update(self,project,key):
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pass
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pass
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class EmptyView (Plot):
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class EmptyView (Plot):
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def __init__(self):
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def __init__(self):
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Plot.__init__(self)
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Plot.__init__(self,None)
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label = gtk.Label('No view')
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label = gtk.Label('No view')
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ebox = gtk.EventBox()
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ebox = gtk.EventBox()
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@ -210,10 +212,10 @@ class EmptyView (Plot):
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self.ebox.hide()
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self.ebox.hide()
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Plot.hide(self)
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Plot.hide(self)
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class SinePlot (Plot):
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class SinePlot(Plot):
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def __init__(self):
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def __init__(self,project):
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Plot.__init__(self)
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Plot.__init__(self,project)
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fig = Figure(figsize=(5,4), dpi=72)
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fig = Figure(figsize=(5,4), dpi=72)
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ax = fig.add_subplot(111)
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ax = fig.add_subplot(111)
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t = arange(0.0,3.0,0.01)
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t = arange(0.0,3.0,0.01)
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@ -228,15 +230,14 @@ class SinePlot (Plot):
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self.toolbar.set_property('show-arrow', False)
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self.toolbar.set_property('show-arrow', False)
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return self.toolbar
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return self.toolbar
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class ScatterPlot (Plot):
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class ScatterPlot(Plot):
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def __init__(self):
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def __init__(self,project):
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Plot.__init__(self)
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Plot.__init__(self,project)
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fig = Figure(figsize=(5,4), dpi=72)
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fig = Figure(figsize=(5,4), dpi=72)
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self.ax = ax = fig.add_subplot(111)
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self.ax = ax = fig.add_subplot(111)
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# testing testing
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# testing testing
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self.c_p = project.c_p
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self.x_dataset = project.datasets[0]
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self.x_dataset = self.c_p.datasets[0]
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x = self.x_dataset._data
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x = self.x_dataset._data
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self.xaxis_data = xaxis_data = x[:,0] + scipy.randn(scipy.shape(x)[0])
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self.xaxis_data = xaxis_data = x[:,0] + scipy.randn(scipy.shape(x)[0])
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self.yaxis_data = yaxis_data = x[:,1]
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self.yaxis_data = yaxis_data = x[:,1]
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@ -286,15 +287,16 @@ class ScatterPlot (Plot):
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logger.log('debug','Selected:\n%s'%index)
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logger.log('debug','Selected:\n%s'%index)
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ids = self.x_dataset.extract_id_from_index('samples',index)
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ids = self.x_dataset.extract_id_from_index('samples',index)
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#update selection object
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#update selection object
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self.c_p.set_selection(self.current_dim,ids)
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self.project.set_selection(self.current_dim,ids)
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logger.log('debug','Selected identifiers:\n%s'%ids)
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logger.log('debug','Selected identifiers:\n%s'%ids)
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def update_selection(self,project):
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def update(self,project,key):
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curr_sel = project.get_selection() # get selection object
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curr_sel = project.get_selection() # get selection object
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ids = curr_sel[self.current_dim] # current identifiers
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ids = curr_sel[self.current_dim] # current identifiers
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index = self.x_dataset.extract_index_from_id(self.current_dim,ids) #conversion to index
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index = self.x_dataset.extract_index_from_id(self.current_dim,ids) #conversion to index
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xdata_new = scipy.take(self.xaxis_data,index) #take data
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xdata_new = scipy.take(self.xaxis_data,index) #take data
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ydata_new = scipy.take(self.yaxis_data,index)
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ydata_new = scipy.take(self.yaxis_data,index)
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self.ax.plot(self.xaxis_data,self.yaxis_data,'ob')
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self.ax.plot(xdata_new,ydata_new,'or')
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self.ax.plot(xdata_new,ydata_new,'or')
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self.canvas.draw()
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self.canvas.draw()
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@ -5,33 +5,35 @@ class Project:
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def __init__(self,name="Testing"):
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def __init__(self,name="Testing"):
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self.name = name
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self.name = name
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self.dim_names = []
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self.dim_names = []
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self._selection_observers = []
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self._observers = {}
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self.current_data=None
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self.current_data=None
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self.datasets=[]
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self.datasets=[]
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self.sel_obj = dataset.Selection()
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self.sel_obj = dataset.Selection()
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def attach(self, observer):
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def attach(self,observer,key):
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"""Attach observer for selection updates"""
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"""Attach observer for selection updates"""
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if not observer in self._selection_observers:
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if not self._observers.has_key(key):
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self._selection_observers.append(observer)
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self._observers[key]=[]
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if not observer in self._observers[key]:
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self._observers[key].append(observer)
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def detach(self, observer):
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def detach(self,observer,key):
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"""Detach observer for selection updates"""
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"""Detach observer for selection updates"""
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try:
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try:
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self.selection_observers.remove(observer)
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self._observers[key].remove(observer)
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except ValueError:
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except ValueError:
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pass
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pass
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def notify(self, modifier=None):
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def notify(self,key,modifier=None):
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"""Notifies observers that selection is updated"""
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"""Notifies observers"""
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for observer in self._selection_observers:
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for observer in self._observers[key]:
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if modifier != observer:
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if modifier != observer:
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observer.update_selection(self)
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observer.update(self,key)
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def set_selection(self,dim_name,selection):
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def set_selection(self,dim_name,selection):
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"""Sets selection and notifies observers"""
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"""Sets a current selection and notify observers"""
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self.sel_obj.current_selection[dim_name] = set(selection)
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self.sel_obj.current_selection[dim_name] = set(selection)
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self.notify()
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self.notify('selection_update')
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def get_selection(self):
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def get_selection(self):
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"""Returns the current selection object"""
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"""Returns the current selection object"""
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@ -50,18 +52,6 @@ class Project:
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dim_name = dim_name + "_t"
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dim_name = dim_name + "_t"
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return dim_name
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return dim_name
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# FIXME: Singleton project should be removed.
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c_p = Project()
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#add test data
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x = scipy.rand(2000,3)
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def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
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test_data = dataset.Dataset(x,def_list)
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c_p.add_dataset(test_data)
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y = scipy.rand(2000,2)
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def_list = [ ['samples',[]], ['yclasses',['C','N']] ]
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test_data = dataset.Dataset(y,def_list)
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c_p.add_dataset(test_data)
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@ -2,8 +2,8 @@ import gtk
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import logger
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import logger
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from annotations import Annotations
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from annotations import Annotations
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from workflow import *
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from workflow import *
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import geneontology
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#import geneontology
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import gostat
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#import gostat
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from scipy import array
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from scipy import array
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class EinarsWorkflow (Workflow):
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class EinarsWorkflow (Workflow):
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