small-fish-gui 1.5.0__tar.gz → 1.6.0__tar.gz

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.5.0
+Version: 1.6.0
 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-1.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.5.0"
+version = "1.6.0"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/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__ = "1.6.0"

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/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-1.5.0 → small_fish_gui-1.6.0}/src/small_fish_gui/gui/prompts.py

@@ -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-1.6.0}/src/small_fish_gui/pipeline/_colocalisation.py

@@ -263,4 +263,13 @@ def launch_colocalisation(result_tables, result_dataframe, colocalisation_distan
         'fraction_spots1_coloc_cluster2' : [fraction_spots1_coloc_cluster2],
     })
 
+    coloc_df['fraction_spots1_coloc_free2'] = coloc_df['fraction_spots1_coloc_spots2'] - coloc_df['fraction_spots1_coloc_cluster2']
+    coloc_df['fraction_spots2_coloc_free1'] = coloc_df['fraction_spots2_coloc_spots1'] - coloc_df['fraction_spots2_coloc_cluster1']
+
+    #Add names
+    coloc_df_col = list(coloc_df.columns)
+    coloc_df['name1'] = acquisition1.at['name']
+    coloc_df['name2'] = acquisition2.at['name']
+    coloc_df = coloc_df.loc[:,['name1','name2'] + coloc_df_col]
+
     return coloc_df

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/src/small_fish_gui/pipeline/_napari_wrapper.py

@@ -13,7 +13,7 @@ from ._colocalisation import spots_multicolocalisation
 
 def _update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, cluster_size, min_spot_number, 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 +25,10 @@ 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] < min_spot_number, 0)
 
     return new_clusters
 
@@ -98,9 +95,8 @@ 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, min_spot_number=min_spot_number, shape=image.shape)
     else : new_clusters = None
 
     return new_spots, new_clusters
@@ -152,9 +148,9 @@ def show_segmentation(
     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-1.6.0}/src/small_fish_gui/pipeline/actions.py

@@ -2,7 +2,7 @@
 This submodule groups all the possible actions of the user in the main windows. It is the start of each action the user can do.
 """
 
-from ..gui.prompts import output_image_prompt, ask_detection_confirmation, ask_cancel_detection
+from ..gui.prompts import output_image_prompt, ask_detection_confirmation, ask_cancel_detection, rename_prompt
 from ..interface.output import write_results
 from ._preprocess import map_channels, prepare_image_detection, reorder_shape, reorder_image_stack
 from .detection import ask_input_parameters, initiate_detection, launch_detection, launch_features_computation, get_nucleus_signal
@@ -177,3 +177,32 @@ def delete_acquisitions(selected_acquisitions : pd.DataFrame,
         result_df = result_df.drop(result_drop_idx, axis=0)
 
     return result_df, cell_result_df, coloc_df
+
+def rename_acquisitions(
+        selected_acquisitions : pd.DataFrame, 
+        result_df : pd.DataFrame, 
+        cell_result_df : pd.DataFrame, 
+        coloc_df : pd.DataFrame
+        ) :
+    
+    if len(result_df) == 0 :
+        sg.popup("No acquisition to rename.")
+        return result_df, cell_result_df, coloc_df
+    
+    if len(selected_acquisitions) == 0 :
+        sg.popup("Please select the acquisitions you would like to rename.")
+
+    else :
+        name = rename_prompt()
+        print("entered : ",name)
+        if not name : return result_df, cell_result_df, coloc_df #User didn't put a name or canceled
+        name : str = name.replace(' ','_')
+        acquisition_ids = list(result_df.iloc[list(selected_acquisitions)]['acquisition_id'])
+
+        result_df.loc[result_df['acquisition_id'].isin(acquisition_ids),['name']] = name
+        if len(cell_result_df) > 0 : cell_result_df.loc[cell_result_df['acquisition_id'].isin(acquisition_ids),['name']] = name
+        if len(coloc_df) > 0 : 
+            coloc_df.loc[coloc_df['acquisition_id_1'].isin(acquisition_ids), ['name1']] = name
+            coloc_df.loc[coloc_df['acquisition_id_2'].isin(acquisition_ids), ['name2']] = name
+
+    return result_df, cell_result_df, coloc_df

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/src/small_fish_gui/pipeline/detection.py

@@ -1,6 +1,7 @@
 """
 Contains code to handle detection as well as bigfish wrappers related to spot detection.
 """
+
 from ._preprocess import ParameterInputError
 from ._preprocess import check_integrity, convert_parameters_types
 from ._signaltonoise import compute_snr_spots
@@ -575,8 +576,6 @@ def launch_cell_extraction(acquisition_id, spots, clusters, image, nucleus_signa
     
     return result_frame
 
-
-
 @add_default_loading
 def launch_clustering(spots, user_parameters): 
 
@@ -694,6 +693,15 @@ def launch_features_computation(acquisition_id, image, nucleus_signal, spots, cl
     frame_results['threshold'] = user_parameters['threshold']
 
     frame_results = pd.DataFrame(columns= frame_results.keys(), data= (frame_results.values(),))
+
+    #Adding name column
+    result_col = list(frame_results.columns)
+    cell_result_col = list(cell_result_dframe.columns)
+    name = "acquisition_{0}".format(acquisition_id)
+    frame_results['name'] = name
+    cell_result_dframe['name'] = name
+    frame_results = frame_results.loc[:,['name'] + result_col]
+    cell_result_dframe = cell_result_dframe.loc[:,['name'] + cell_result_col]
         
     return frame_results, cell_result_dframe
 

{small_fish_gui-1.5.0 → small_fish_gui-1.6.0}/src/small_fish_gui/pipeline/main.py

@@ -5,7 +5,7 @@ This script is called when software starts; it is the main loop.
 import pandas as pd
 import PySimpleGUI as sg
 from ..gui import hub_prompt
-from .actions import add_detection, save_results, compute_colocalisation, delete_acquisitions
+from .actions import add_detection, save_results, compute_colocalisation, delete_acquisitions, rename_acquisitions
 from ._preprocess import clean_unused_parameters_cache
 from ..batch import batch_promp
 
@@ -84,6 +84,10 @@ while True : #Break this loop to close small_fish
                 preset=user_parameters,
             )
         
+        elif event == "Rename acquisition" :
+            selected_acquisitions = values.setdefault('result_table', []) #Contains the lines selected by the user on the sum-up array.
+            result_df, cell_result_df, coloc_df = rename_acquisitions(selected_acquisitions, result_df, cell_result_df, coloc_df)
+
         else :
             break