FIXING STUFF!

Rename should be complete or almost so.

laydi/annotations.py

@@ -1,5 +1,5 @@
 
-from fluents import dataset
+from laydi import dataset
 
 _dim_annotation_handlers = {}
 

laydi/dataset.py

@@ -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

laydi/dialogs.py

@@ -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.

laydi/laydi.glade

@@ -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; &quot;a yacht with long, fluent curves&quot;
+1: easy and graceful in shape; &quot;a yacht with long, laydi curves&quot;
 
 2: smooth and unconstrained in movement; &quot;a long, smooth stride&quot;; &quot;the fluid motion of a cat&quot;; &quot;the liquid grace of a ballerina&quot;; &quot;liquid prose&quot; [syn:{flowing}, {fluid}, {liquid}, {smooth}]
 
@@ -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>

laydi/laydi.py

@@ -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:

laydi/lib/blmfuncs.py

@@ -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"

laydi/lib/blmplots.py

@@ -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

laydi/navigator.py

@@ -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)

laydi/plots.py

@@ -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)

laydi/project.py

@@ -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)

laydi/view.py

@@ -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]:

laydi/workflow.py

@@ -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))