small-fish-gui 1.5.0__tar.gz → 1.7.0__tar.gz

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.5.0
+Version: 1.7.0
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/2Echoes/small_fish
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.5.0"
+version = "1.7.0"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/src/small_fish_gui/__init__.py

@@ -38,4 +38,4 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 """
-__version__ = "1.5.0"
+__version__ = "1.7.0"

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/src/small_fish_gui/__main__.py

@@ -1,6 +1,8 @@
 import sys, subprocess
 import PySimpleGUI as sg
 
+from small_fish_gui import __version__
+
 def main():
     import small_fish_gui.pipeline.main
 
@@ -10,9 +12,7 @@ def is_last_version() :
     latest_version = latest_version[:latest_version.find(')')]
     latest_version = latest_version.replace(' ','').split(',')[-1]
 
-    current_version = str(subprocess.run([sys.executable, '-m', 'pip', 'show', '{}'.format('small_fish_gui')], capture_output=True, text=True))
-    current_version = current_version[current_version.find('Version:')+8:]
-    current_version = current_version[:current_version.find('\\n')].replace(' ','')
+    current_version = __version__
 
     return current_version == latest_version
 

small_fish_gui-1.7.0/src/small_fish_gui/gui/_napari_widgets.py

@@ -0,0 +1,93 @@
+"""
+Submodule containing custom class for napari widgets
+"""
+import numpy as np
+from napari.layers import Labels
+from magicgui import magicgui
+
+class cell_label_eraser :
+    """
+    Must be instanced within Napari Viewer definition range for update connection to work, cell deletion works fine anyway.
+    """
+    def __init__(self, label_list: 'list[Labels]'):
+        self.widget = self._create_eraser(label_list)
+        for label_layer in label_list :
+            label_layer.events.selected_label.connect((self, 'update'))
+
+    def update(self, event) :
+        layer : Labels = event.source
+        new_label = layer.selected_label
+        self.widget.label_number.value = new_label
+        self.widget.update()
+    
+    def _create_eraser(self, label_list: 'list[Labels]') :
+        @magicgui(
+                call_button="Delete cell",
+                auto_call=False
+                )
+        def label_eraser(label_number: int) -> None :
+
+            for i, label in enumerate(label_list) :
+                label_list[i].data[label.data == label_number] = 0
+                label.refresh()
+
+        return label_eraser
+
+
+
+class free_label_picker :
+    def __init__(self, label_list):
+        self.widget = self._create_free_label_picker(label_list)
+    
+    def _create_free_label_picker(self, label_list : 'list[Labels]') :
+        @magicgui(
+            call_button="Pick free label",
+            auto_call=False
+        )
+        def label_pick()->None :
+            max_list = [label_layer.data.max() for label_layer in label_list]
+            new_label = max(max_list) + 1
+            for label_layer in label_list :
+                label_layer.selected_label = new_label
+                label_layer.refresh()
+
+        return label_pick
+
+
+class segmentation_reseter :
+    def __init__(self, label_list):
+        self.save = self._get_save(label_list)
+        self.widget = self._create_widget(label_list)
+        
+    
+    def _get_save(self, label_list : 'list[Labels]') :
+        return [label.data.copy() for label in label_list]
+
+    def _create_widget(self, label_list: 'list[Labels]') :
+        @magicgui(
+            call_button= 'Reset segmentation',
+            auto_call=False,
+        )
+        def reset_segmentation() -> None:
+            for save_data, layer in zip(self.save, label_list) :
+                layer.data = save_data.copy()
+                layer.refresh()
+
+        return reset_segmentation
+
+class changes_propagater :
+    def __init__(self, label_list):
+        self.widget = self._create_widget(label_list)
+
+    def _create_widget(self, label_list: 'list[Labels]') :
+        @magicgui(
+            call_button='Apply changes',
+            auto_call=False,
+        )
+        def apply_changes() -> None:
+            for layer in label_list :
+                slices = layer.data.shape[0]
+                layer_2D = np.max(layer.data, axis=0)
+                layer.data = np.repeat(layer_2D[np.newaxis], slices, axis=0)
+                layer.refresh()
+        return apply_changes

small_fish_gui-1.5.0/src/small_fish_gui/pipeline/_napari_wrapper.py → small_fish_gui-1.7.0/src/small_fish_gui/gui/napari.py

@@ -7,13 +7,21 @@ import napari.types
 import numpy as np
 import napari
 
+from napari.layers import Labels
+
+from magicgui import widgets
+from magicgui import magicgui
+
 from bigfish.stack import check_parameter
+from ._napari_widgets import cell_label_eraser, segmentation_reseter, changes_propagater, free_label_picker
 from ..utils import compute_anisotropy_coef
-from ._colocalisation import spots_multicolocalisation
+from ..pipeline._colocalisation import spots_multicolocalisation
+
+#Post detection
 
-def _update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, cluster_size, min_spot_number, shape) :
+def _update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, cluster_size, shape) :
     if len(new_clusters) == 0 : return new_clusters
-    if len(spots) == 0 : return new_clusters
+    if len(spots) == 0 : return np.empty(shape=(0,2+len(voxel_size)))
 
     if len(new_clusters[0]) in [2,3] :
         new_clusters = np.concatenate([
@@ -25,13 +33,10 @@ def _update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, cl
     assert len(new_clusters[0]) == 4 or len(new_clusters[0]) == 5, "Wrong number of coordinates for clusters should not happen."
     
     # Update spots clusters
-    if len(voxel_size) == 3 :
-        new_clusters[:,-2] = spots_multicolocalisation(new_clusters[:,:3], spots, radius_nm= cluster_size, voxel_size=voxel_size, image_shape=shape)
-    elif len(voxel_size) == 2 :
-        new_clusters[:,-2] = spots_multicolocalisation(new_clusters[:,:2], spots, radius_nm= cluster_size, voxel_size=voxel_size, image_shape=shape)
+    new_clusters[:,-2] = spots_multicolocalisation(new_clusters[:,:-2], spots, radius_nm= cluster_size, voxel_size=voxel_size, image_shape=shape)
 
     # delete too small clusters
-        new_clusters = np.delete(new_clusters, new_clusters[:,-2] < min_spot_number, 0)
+    new_clusters = np.delete(new_clusters, new_clusters[:,-2] == 0, 0)
 
     return new_clusters
 
@@ -98,13 +103,16 @@ def correct_spots(image, spots, voxel_size= (1,1,1), clusters= None, cluster_siz
     new_spots = np.array(Viewer.layers['single spots'].data, dtype= int)
 
     if type(clusters) != type(None) :
-        if len(clusters) > 0 : 
-            new_clusters = np.array(Viewer.layers['foci'].data, dtype= int)
-            new_clusters = _update_clusters(new_clusters, new_spots, voxel_size=voxel_size, cluster_size=cluster_size, min_spot_number=min_spot_number, shape=image.shape)
+        new_clusters = np.array(Viewer.layers['foci'].data, dtype= int)
+        new_clusters = _update_clusters(new_clusters, new_spots, voxel_size=voxel_size, cluster_size=cluster_size, shape=image.shape)
     else : new_clusters = None
 
     return new_spots, new_clusters
 
+# Segmentation
+    
+
+
 def show_segmentation(
         nuc_image : np.ndarray,
         nuc_label : np.ndarray,
@@ -135,26 +143,40 @@ def show_segmentation(
             )
 
     #Init Napari viewer
-    Viewer = napari.Viewer(ndisplay=2, title= 'Show segmentation', axis_labels=['z','y','x'] if dim == 3 else ['y', 'x'], show= False)
+    Viewer = napari.Viewer(ndisplay=2, title= 'Show segmentation', axis_labels=['z','y','x'] if dim == 3 else ['y', 'x'])
     
-    # Adding channels
+    # Adding nuclei
     nuc_signal_layer = Viewer.add_image(nuc_image, name= "nucleus signal", blending= 'additive', colormap='blue', contrast_limits=[nuc_image.min(), nuc_image.max()])
-    nuc_label_layer = Viewer.add_labels(nuc_label, opacity= 0.5, blending= 'additive', name= 'nucleus_label',)
+    nuc_label_layer = Viewer.add_labels(nuc_label, opacity= 0.6, name= 'nucleus_label',)
     nuc_label_layer.preserve_labels = True
+    labels_layer_list = [nuc_label_layer]
     
-    #Adding labels
-    if type(cyto_image) != type(None) : Viewer.add_image(cyto_image, name= "cytoplasm signal", blending= 'additive', colormap='red', contrast_limits=[cyto_image.min(), cyto_image.max()])
+    #Adding cytoplasm
     if (type(cyto_label) != type(None) and not np.array_equal(cyto_label, nuc_label) ) or (type(cyto_label) != type(None) and cyto_label.max() == 0): 
-        cyto_label_layer = Viewer.add_labels(cyto_label, opacity= 0.4, blending= 'additive', name= 'cytoplasm_label')
+        Viewer.add_image(cyto_image, name= "cytoplasm signal", blending= 'additive', colormap='red', contrast_limits=[cyto_image.min(), cyto_image.max()])
+        cyto_label_layer = Viewer.add_labels(cyto_label, opacity= 0.6, name= 'cytoplasm_label')
         cyto_label_layer.preserve_labels = True
-    
+        labels_layer_list += [cyto_label_layer]
+
+    #Adding widget
+    label_eraser = cell_label_eraser(labels_layer_list)
+    label_picker = free_label_picker(labels_layer_list)
+    label_reseter = segmentation_reseter(labels_layer_list)
+    changes_applier = changes_propagater(labels_layer_list)
+
+    buttons_container = widgets.Container(widgets=[label_picker.widget, changes_applier.widget, label_reseter.widget], labels=False, layout='horizontal')
+    tools_container = widgets.Container(
+        widgets = [buttons_container, label_eraser.widget],
+        labels=False,
+    )
+    Viewer.window.add_dock_widget(tools_container, name='SmallFish', area='left')
+
     #Launch Napari
-    Viewer.show(block=False)
     napari.run()
 
-
     new_nuc_label = Viewer.layers['nucleus_label'].data
-    if type(cyto_label) != type(None) and not np.array_equal(cyto_label, nuc_label) : new_cyto_label = Viewer.layers['cytoplasm_label'].data
+    if 'cytoplasm_label' in Viewer.layers : 
+        new_cyto_label = Viewer.layers['cytoplasm_label'].data
     else : new_cyto_label = new_nuc_label
 
     return new_nuc_label, new_cyto_label

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/src/small_fish_gui/gui/prompts.py

@@ -136,8 +136,8 @@ def output_image_prompt(filename) :
         excel_filename = values['filename'] + ".xlsx"
         feather_filename = values['filename'] + ".feather"
 
-        if not values['Excel'] and not values['Feather'] :
-            sg.popup("Please check at least one box : Excel/Feather")
+        if not values['Excel'] and not values['Feather'] and not values['csv'] :
+            sg.popup("Please check at least one box : Excel/Feather/csv")
             relaunch = True
         elif not os.path.isdir(values['folder']) :
             sg.popup("Incorrect folder")
@@ -280,7 +280,7 @@ def _warning_popup(warning:str) :
 
 def _sumup_df(results: pd.DataFrame) :
 
-    COLUMNS = ['acquisition_id','threshold', 'spot_number', 'cell_number', 'filename', 'channel to compute']
+    COLUMNS = ['acquisition_id','name','threshold', 'spot_number', 'cell_number', 'filename', 'channel to compute']
 
     if len(results) > 0 :
         if 'channel to compute' not in results : results['channel to compute'] = np.NaN
@@ -303,7 +303,7 @@ def hub_prompt(fov_results, do_segmentation=False) :
         [sg.Text('RESULTS', font= 'bold 13')],
         [sg.Table(values= list(sumup_df.values), headings= list(sumup_df.columns), row_height=20, num_rows= 5, vertical_scroll_only=False, key= "result_table"), segmentation_object],
         [sg.Button('Add detection'), sg.Button('Compute colocalisation'), sg.Button('Batch detection')],
-        [sg.Button('Save results', button_color= 'green'), sg.Button('Delete acquisitions',button_color= 'gray'), sg.Button('Reset segmentation',button_color= 'gray'), sg.Button('Reset results',button_color= 'gray')]
+        [sg.Button('Rename acquisition', button_color= 'green'), sg.Button('Save results', button_color= 'green'), sg.Button('Delete acquisitions',button_color= 'gray'), sg.Button('Reset segmentation',button_color= 'gray'), sg.Button('Reset results',button_color= 'gray')]
         # [sg.Button('Save results', button_color= 'green'), sg.Button('Reset results',button_color= 'gray')]
     ]
 
@@ -318,16 +318,20 @@ def hub_prompt(fov_results, do_segmentation=False) :
             return event, values
 
 def coloc_prompt() :
-    layout = [
-        [parameters_layout(['colocalisation distance'], header= 'Colocalisation', default_values= 0)]
-    ]
-
+    layout = parameters_layout(['colocalisation distance'], unit= 'nm', header= 'Colocalisation', default_values= 0)
     event, values = prompt_with_help(layout)
 
     if event == 'Ok' :
         return values['colocalisation distance']
     else : return False
 
+def rename_prompt() :
+    layout = parameters_layout(['name'], header= "Rename acquisitions", size=12)
+    event, values = prompt_with_help(layout)
+    if event == 'Ok' :
+        return values['name']
+    else : return False
+
 def ask_detection_confirmation(used_threshold) :
     layout = [
         [sg.Text("Proceed with current detection ?", font= 'bold 10')],

{small_fish_gui-1.5.0 → small_fish_gui-1.7.0}/src/small_fish_gui/interface/output.py

@@ -10,11 +10,9 @@ def _cast_spot_to_tuple(spot) :
 def _cast_spots_to_tuple(spots) :
     return tuple(list(map(_cast_spot_to_tuple, spots)))
 
-def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= True, do_feather= False, do_csv=False, overwrite=False) :
+def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= True, do_feather= False, do_csv=False, overwrite=False, reset_index=True) :
     check_parameter(dataframe= pd.DataFrame, path= str, filename = str, do_excel = bool, do_feather = bool)
 
-    dataframe.columns = dataframe.columns.astype(str) # assert columns header are string for feather
-
     if len(dataframe) == 0 : return True
     if not do_excel and not do_feather and not do_csv : 
         return False
@@ -22,6 +20,14 @@ def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= Tru
     if not path.endswith('/') : path +='/'
     assert os.path.isdir(path)
 
+    #Casting cols name to str for feather format
+    index_dim = dataframe.columns.nlevels
+    if index_dim == 1 :
+        dataframe.columns = dataframe.columns.astype(str)
+    else :
+        casted_cols = [dataframe.columns.get_level_values(level).astype(str) for level in range(index_dim)]
+        casted_cols = zip(*casted_cols)
+        dataframe.columns = pd.MultiIndex.from_tuples(casted_cols)
 
     new_filename = filename
     i= 1
@@ -31,23 +37,21 @@ def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= Tru
             new_filename = filename + '_{0}'.format(i)
             i+=1
 
-    if 'image' in dataframe.columns :
-        dataframe = dataframe.drop(['image'], axis=1)
+    COLUMNS_TO_DROP = ['image', 'spots', 'clusters', 'rna_coords', 'cluster_coords']
+    for col in COLUMNS_TO_DROP :
+        dataframe = dataframe.drop(columns=col)
 
-    if 'spots' in dataframe.columns : 
-        dataframe = dataframe.drop(['spots'], axis= 1)
-        
-    if 'clusters' in dataframe.columns : 
-        dataframe = dataframe.drop(['clusters'], axis= 1)
+    if reset_index : dataframe = dataframe.reset_index(drop=True)
 
-    if do_feather : dataframe.reset_index(drop=True).to_feather(path + new_filename + '.feather')
-    if do_csv : dataframe.reset_index(drop=True).to_csv(path + new_filename + '.csv', sep=";")
+    if do_csv : dataframe.to_csv(path + new_filename + '.csv', sep=";")
     if do_excel : 
         if len(dataframe) < MAX_LEN_EXCEL :
-            dataframe.reset_index(drop=True).to_excel(path + new_filename + '.xlsx')
+            dataframe.to_excel(path + new_filename + '.xlsx')
         else : 
             print("Error : Table too big to be saved in excel format.")
             return False
     
+    if do_feather : 
+        dataframe.to_parquet(path + new_filename + '.parquet')
 
-    return True
+    return True