def test_kwik_loader_1(): # Open the mock data. dir = TEST_FOLDER xmlfile = os.path.join(dir, 'test.xml') l = KwikLoader(filename=xmlfile) # Get full data sets. features = l.get_features() # features_some = l.get_some_features() masks = l.get_masks() waveforms = l.get_waveforms() clusters = l.get_clusters() spiketimes = l.get_spiketimes() nclusters = len(Counter(clusters)) # probe = l.get_probe() cluster_colors = l.get_cluster_colors() cluster_groups = l.get_cluster_groups() group_colors = l.get_group_colors() group_names = l.get_group_names() cluster_sizes = l.get_cluster_sizes() # Check the shape of the data sets. # --------------------------------- assert check_shape(features, (nspikes, nchannels * fetdim + 1)) # assert features_some.shape[1] == nchannels * fetdim + 1 assert check_shape(masks, (nspikes, nchannels * fetdim + 1)) assert check_shape(waveforms, (nspikes, nsamples, nchannels)) assert check_shape(clusters, (nspikes,)) assert check_shape(spiketimes, (nspikes,)) # assert check_shape(probe, (nchannels, 2)) assert check_shape(cluster_colors, (nclusters,)) assert check_shape(cluster_groups, (nclusters,)) assert check_shape(group_colors, (4,)) assert check_shape(group_names, (4,)) assert check_shape(cluster_sizes, (nclusters,)) # Check the data type of the data sets. # ------------------------------------- assert check_dtype(features, np.float32) assert check_dtype(masks, np.float32) # HACK: Panel has no dtype(s) attribute # assert check_dtype(waveforms, np.float32) assert check_dtype(clusters, np.int32) assert check_dtype(spiketimes, np.float64) # assert check_dtype(probe, np.float32) assert check_dtype(cluster_colors, np.int32) assert check_dtype(cluster_groups, np.int32) assert check_dtype(group_colors, np.int32) assert check_dtype(group_names, object) assert check_dtype(cluster_sizes, np.int32) l.close()
def test_kwik_save(): """WARNING: this test should occur at the end of the module since it changes the mock data sets.""" # Open the mock data. dir = TEST_FOLDER xmlfile = os.path.join(dir, 'test.xml') l = KwikLoader(filename=xmlfile) clusters = l.get_clusters() cluster_colors = l.get_cluster_colors() cluster_groups = l.get_cluster_groups() group_colors = l.get_group_colors() group_names = l.get_group_names() # Set clusters. indices = get_indices(clusters) l.set_cluster(indices[::2], 2) l.set_cluster(indices[1::2], 3) # Set cluster info. cluster_indices = l.get_clusters_unique() l.set_cluster_colors(cluster_indices[::2], 10) l.set_cluster_colors(cluster_indices[1::2], 20) l.set_cluster_groups(cluster_indices[::2], 1) l.set_cluster_groups(cluster_indices[1::2], 0) # Save. l.remove_empty_clusters() l.save() clusters = l.get_clusters() cluster_colors = l.get_cluster_colors() cluster_groups = l.get_cluster_groups() group_colors = l.get_group_colors() group_names = l.get_group_names() assert np.all(clusters[::2] == 2) assert np.all(clusters[1::2] == 3) assert np.all(cluster_colors[::2] == 10) assert np.all(cluster_colors[1::2] == 20) print cluster_groups assert np.all(cluster_groups[::2] == 1) assert np.all(cluster_groups[1::2] == 0) l.close()
def __init__(self, parent=None, dolog=True, filename=None): super(KwikSkope, self).__init__(parent) # HACK: display the icon in Windows' taskbar. if os.name == 'nt': try: import ctypes myappid = 'klustateam.kwikskope' ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID( myappid) except: pass self.dolog = dolog if self.dolog: create_file_logger() log.debug("Using {0:s}.".format(QT_BINDING)) # Main window options. self.move(50, 50) self.setWindowTitle('KwikSkope') # Focus options. self.setFocusPolicy(QtCore.Qt.WheelFocus) self.setMouseTracking(True) # Dock widgets options. self.setDockNestingEnabled(True) self.setAnimated(False) self.setWindowIcon(get_icon('logo')) # Initialize some variables. # self.statscache = None # self.loader = KlustersLoader() self.loader = KwikLoader() self.loader.progressReported.connect(self.open_progress_reported) self.loader.saveProgressReported.connect(self.save_progress_reported) self.wizard = Wizard() self.controller = None self.spikes_highlighted = [] self.spikes_selected = [] self._wizard = False self.is_file_open = False self.need_save = False self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor) self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor) self.is_busy = False self.override_color = False self.computing_correlograms = False self.computing_matrix = False # Create the main window. self.create_views() self.create_file_actions() self.create_edit_actions() self.create_view_actions() self.create_help_actions() self.create_menu() self.create_toolbar() self.create_open_progress_dialog() self.create_save_progress_dialog() self.create_threads() # Update action enabled/disabled property. self.update_action_enabled() # Show the main window. self.set_styles() self.restore_geometry() # Automatically load a file upon startup if requested. if filename: filename = os.path.realpath(filename) self.open_task.open(self.loader, filename) self.show()
def test_kwik_loader_control(): # Open the mock data. dir = TEST_FOLDER xmlfile = os.path.join(dir, 'test.xml') l = KwikLoader(filename=xmlfile) # Take all spikes in cluster 3. spikes = get_indices(l.get_clusters(clusters=3)) # Put them in cluster 4. l.set_cluster(spikes, 4) spikes_new = get_indices(l.get_clusters(clusters=4)) # Ensure all spikes in old cluster 3 are now in cluster 4. assert np.all(np.in1d(spikes, spikes_new)) # Change cluster groups. clusters = [2, 3, 4] group = 0 l.set_cluster_groups(clusters, group) groups = l.get_cluster_groups(clusters) assert np.all(groups == group) # Change cluster colors. clusters = [2, 3, 4] color = 12 l.set_cluster_colors(clusters, color) colors = l.get_cluster_colors(clusters) assert np.all(colors == color) # Change group name. group = 0 name = l.get_group_names(group) name_new = 'Noise new' assert name == 'Noise' l.set_group_names(group, name_new) assert l.get_group_names(group) == name_new # Change group color. groups = [1, 2] colors = l.get_group_colors(groups) color_new = 10 l.set_group_colors(groups, color_new) assert np.all(l.get_group_colors(groups) == color_new) # Add cluster and group. spikes = get_indices(l.get_clusters(clusters=3))[:10] # Create new group 100. l.add_group(100, 'New group', 10) # Create new cluster 10000 and put it in group 100. l.add_cluster(10000, 100, 10) # Put some spikes in the new cluster. l.set_cluster(spikes, 10000) clusters = l.get_clusters(spikes=spikes) assert np.all(clusters == 10000) groups = l.get_cluster_groups(10000) assert groups == 100 l.set_cluster(spikes, 2) # Remove the new cluster and group. l.remove_cluster(10000) l.remove_group(100) assert np.all(~np.in1d(10000, l.get_clusters())) assert np.all(~np.in1d(100, l.get_cluster_groups())) l.close()