small-fish-gui 1.4.0__tar.gz → 1.6.0__tar.gz

{small_fish_gui-1.4.0 → small_fish_gui-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.4.0
+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-1.4.0 → small_fish_gui-1.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.4.0"
+version = "1.6.0"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

small_fish_gui-1.6.0/src/small_fish_gui/.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+   - epub

{small_fish_gui-1.4.0 → small_fish_gui-1.6.0}/src/small_fish_gui/README.md

@@ -5,7 +5,7 @@ Cell segmentation (**2D**) is peformed using *cellpose* (published work) : https
 
 Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
 
-Time stacks are not yet supported.
+**Time stacks are not supported.**
 
 ## What can you do with small fish ?
 
@@ -77,7 +77,7 @@ If you run into any problems I would recommend following the official cellpose i
 
 
 ### Training cellpose
-If you want to train your own cellpose model or import custom model from exterior source I recommend doing so from the cellpose GUI 
+If you want to train your own cellpose model or import custom model from exterior source I recommend doing so from the cellpose GUI. Note that Small fish uses mean projection to segment images in 2D, if you want to retrain a cellpose model to fit your data it is recommended to do so on mean or max projection of your data.
 
 To install the GUI run : 
 
@@ -93,6 +93,5 @@ Note that for training it is recommended to first set up your GPU as training co
 ## Developpement
 
 Optional features to include in future versions : 
-- batch processing
 - time stack (which would include cell tracking)
 - 3D segmentation

{small_fish_gui-1.4.0 → 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__ = "1.4.0"
+__version__ = "1.6.0"

{small_fish_gui-1.4.0 → 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-1.4.0 → small_fish_gui-1.6.0}/src/small_fish_gui/batch/prompt.py

@@ -35,7 +35,7 @@ def batch_promp(
     sanity_header = sg.Text("Dimension sanity", font=('bold',15), pad=(0,10))
     dimension_number_text = sg.Text("Dimension number : unknown")
     
-
+#LAYOUT INIT
 #########################################
 #####   COLUMNS
 #########################################
@@ -182,8 +182,6 @@ def batch_promp(
         [tab_col, launch_col],
         [stream_output],
     ]
-    stream_output.restore_stderr()
-    stream_output.restore_stdout()
 
     window = sg.Window("small fish", layout=layout, size= (800,800), auto_size_buttons=True, auto_size_text=True, resizable=True)
     
@@ -332,7 +330,11 @@ def batch_promp(
                 batch_name_input.update(value=values.get('batch_name'))
 
             elif event == "Cancel" :
-                raise InterruptedError("cancel")
+                stream_output.restore_stderr()
+                stream_output.restore_stdout()
+                window.close()
+                return results_df, cell_results_df, acquisition_id, preset, False, None,None #Segmentation done : False, cell label : None, Nucleus label : None
+
 
             elif event == None :
                 raise InterruptedError("closed")

small_fish_gui-1.6.0/src/small_fish_gui/docs/conf.py

@@ -0,0 +1 @@
+#init conf file

{small_fish_gui-1.4.0 → small_fish_gui-1.6.0}/src/small_fish_gui/gui/layout.py

@@ -95,7 +95,7 @@ def path_layout(keys= [],look_for_dir = False, header=None, preset=os.getcwd())
 
     max_length = len(max(keys, key=len))
     layout = [
-        [sg.Text(pad_right(name, max_length, ' ')), Browse(key= name, initial_folder= preset)] for name in keys
+        [sg.Text(pad_right(name, max_length, ' ')), Browse(key= name, target=(555666777,2), initial_folder= preset), sg.Text('')] for name in keys
         ]
     if isinstance(header, str) :
         layout = [add_header(header)] + layout
@@ -152,7 +152,20 @@ def radio_layout(values, header=None) :
         layout = [add_header(header)] + layout
     return layout
 
-def _segmentation_layout(multichannel, cytoplasm_model_preset= 'cyto2', nucleus_model_preset= 'nuclei', cytoplasm_channel_preset=0, nucleus_channel_preset=0, cyto_diameter_preset=30, nucleus_diameter_preset= 30, show_segmentation_preset= False, segment_only_nuclei_preset=False, saving_path_preset=os.getcwd(), filename_preset='cell_segmentation.png',) :
+def _segmentation_layout(
+        multichannel, 
+        cytoplasm_model_preset= 'cyto3', 
+        nucleus_model_preset= 'nuclei', 
+        cytoplasm_channel_preset=0, 
+        nucleus_channel_preset=0, 
+        other_nucleus_image_preset = None,
+        cyto_diameter_preset=30, 
+        nucleus_diameter_preset= 30, 
+        show_segmentation_preset= False, 
+        segment_only_nuclei_preset=False, 
+        saving_path_preset=os.getcwd(), 
+        filename_preset='cell_segmentation.png',
+        ) :
     
     USE_GPU = use_gpu()
 
@@ -160,7 +173,9 @@ def _segmentation_layout(multichannel, cytoplasm_model_preset= 'cyto2', nucleus_
     if len(models_list) == 0 : models_list = ['no model found']
     
     #Header : GPU availabality
-    layout = [[sg.Text("GPU is currently "), sg.Text('ON', text_color= 'green') if USE_GPU else sg.Text('OFF', text_color= 'red')]]
+    layout = [
+        [sg.Text("GPU is currently "), sg.Text('ON', text_color= 'green') if USE_GPU else sg.Text('OFF', text_color= 'red')]
+        ]
     
     #cytoplasm parameters
     layout += [
@@ -170,6 +185,8 @@ def _segmentation_layout(multichannel, cytoplasm_model_preset= 'cyto2', nucleus_
                         ]
                         
     if multichannel : layout += parameters_layout(['cytoplasm channel'],default_values= [cytoplasm_channel_preset])
+
+
     layout += parameters_layout(['cytoplasm diameter'], unit= "px", default_values= [cyto_diameter_preset])
     #Nucleus parameters
     layout += [
@@ -179,6 +196,7 @@ def _segmentation_layout(multichannel, cytoplasm_model_preset= 'cyto2', nucleus_
                 ]
     
     if multichannel : layout += parameters_layout(['nucleus channel'], default_values= [nucleus_channel_preset])
+    layout += path_layout(['other_nucleus_image'], preset=other_nucleus_image_preset)
     layout += parameters_layout([ 'nucleus diameter'],unit= "px", default_values= [nucleus_diameter_preset])
     layout += bool_layout(["Segment only nuclei"], preset=segment_only_nuclei_preset)
     

{small_fish_gui-1.4.0 → small_fish_gui-1.6.0}/src/small_fish_gui/gui/prompts.py

@@ -32,14 +32,14 @@ def prompt(layout, add_ok_cancel=True, timeout=None, timeout_key='TIMEOUT_KEY',
         window.close()
         return event, values
 
-def prompt_with_help(layout, help =None, add_scrollbar=True) :
+def prompt_with_help(layout, help =None, add_scrollbar=True, vertical_scroll_only=True) :
     layout += [[]]
     layout += [[sg.Button('Help')]]
     layout += [[sg.Button('Ok'), sg.Button('Cancel')]]
     
     if add_scrollbar :
         size = (400,500)
-        col_elmt = sg.Column(layout, scrollable=True, vertical_scroll_only=True, size=size)
+        col_elmt = sg.Column(layout, scrollable=True, vertical_scroll_only=vertical_scroll_only, size=size)
         layout = [[col_elmt]]
     else :
         size = (None,None)
@@ -280,11 +280,13 @@ def _warning_popup(warning:str) :
 
 def _sumup_df(results: pd.DataFrame) :
 
+    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
-        res = results.loc[:,['acquisition_id', 'spot_number', 'cell_number', 'filename', 'channel to compute']]
+        res = results.loc[:,COLUMNS]
     else :
-        res = pd.DataFrame(columns= ['acquisition_id', 'spot_number', 'cell_number', 'filename', 'channel to compute'])
+        res = pd.DataFrame(columns= COLUMNS)
 
     return res
 
@@ -293,15 +295,15 @@ def hub_prompt(fov_results, do_segmentation=False) :
     sumup_df = _sumup_df(fov_results)
     
     if do_segmentation :
-        segmentation_object = sg.Text('Segmentation was performed', font='8', text_color= 'green')
+        segmentation_object = sg.Text('Segmentation in memory', font='8', text_color= 'green')
     else :
-        segmentation_object = sg.Text('Segmentation was not performed', font='8', text_color= 'red')
+        segmentation_object = sg.Text('No segmentation in memory', font='8', text_color= 'red')
 
     layout = [
         [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')]
     ]
 
@@ -316,16 +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-1.4.0 → 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-1.6.0/src/small_fish_gui/pipeline/_napari_wrapper.py

@@ -0,0 +1,198 @@
+"""
+Contains Napari wrappers to visualise and correct spots/clusters.
+"""
+
+import napari.layers
+import napari.types
+import numpy as np
+import napari
+
+from bigfish.stack import check_parameter
+from ..utils import compute_anisotropy_coef
+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 np.empty(shape=(0,2+len(voxel_size)))
+
+    if len(new_clusters[0]) in [2,3] :
+        new_clusters = np.concatenate([
+            new_clusters,
+            np.zeros(shape=(len(new_clusters),1), dtype=int),
+            np.arange(len(new_clusters), dtype=int).reshape(len(new_clusters),1)
+            ],axis=1, dtype=int)
+
+    assert len(new_clusters[0]) == 4 or len(new_clusters[0]) == 5, "Wrong number of coordinates for clusters should not happen."
+    
+    # Update spots clusters
+    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)
+
+    return new_clusters
+
+def correct_spots(image, spots, voxel_size= (1,1,1), clusters= None, cluster_size=None, min_spot_number=0, cell_label= None, nucleus_label= None, other_images =[]):
+    """
+    Open Napari viewer for user to visualize and corrects spots, clusters.
+
+    Returns
+    -------
+        new_spots,new_clusters
+    """
+    check_parameter(image= np.ndarray, voxel_size= (tuple,list))
+    dim = len(voxel_size)
+
+    if dim == 3 and type(cell_label) != type(None) :
+        cell_label = np.repeat(
+            cell_label[np.newaxis],
+            repeats= len(image),
+            axis=0
+        )
+    if dim == 3 and type(nucleus_label) != type(None) :
+        nucleus_label = np.repeat(
+            nucleus_label[np.newaxis],
+            repeats= len(image),
+            axis=0
+        )
+
+    scale = compute_anisotropy_coef(voxel_size)
+    Viewer = napari.Viewer(ndisplay=2, title= 'Spot correction', axis_labels=['z','y','x'], show= False)
+    Viewer.add_image(image, scale=scale, name= "rna signal", blending= 'additive', colormap='red', contrast_limits=[image.min(), image.max()])
+    other_colors = ['green', 'blue', 'gray', 'cyan', 'bop orange', 'bop purple'] * ((len(other_images)-1 // 7) + 1)
+    for im, color in zip(other_images, other_colors) : 
+        Viewer.add_image(im, scale=scale, blending='additive', visible=False, colormap=color, contrast_limits=[im.min(), im.max()])
+    layer_offset = len(other_images)
+
+    Viewer.add_points(  # single molecule spots; this layer can be update by user.
+        spots, 
+        size = 5, 
+        scale=scale, 
+        face_color= 'transparent', 
+        opacity= 1, 
+        symbol= 'disc', 
+        name= 'single spots'
+        )
+    
+    if type(clusters) != type(None) : Viewer.add_points( # cluster; this layer can be update by user.
+        clusters[:,:dim], 
+        size = 10, 
+        scale=scale, 
+        face_color= 'blue', 
+        opacity= 0.7, 
+        symbol= 'diamond', 
+        name= 'foci', 
+        features= {"spot_number" : clusters[:,dim], "id" : clusters[:,dim+1]}, 
+        feature_defaults= {"spot_number" : 0, "id" : -1}
+        )
+
+    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
+    if type(nucleus_label) != type(None) : Viewer.add_labels(nucleus_label, scale=scale, opacity= 0.2, blending= 'additive')
+        
+    Viewer.show(block=False)
+    napari.run()
+
+    new_spots = np.array(Viewer.layers['single spots'].data, dtype= int)
+
+    if type(clusters) != type(None) :
+        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
+
+def show_segmentation(
+        nuc_image : np.ndarray,
+        nuc_label : np.ndarray,
+        cyto_image : np.ndarray = None,
+        cyto_label : np.ndarray = None,
+) :
+    dim = nuc_image.ndim
+    
+    if type(cyto_image) != type(None) :
+        if cyto_image.ndim != nuc_image.ndim : raise ValueError("Cyto and Nuc dimensions missmatch.")
+        if type(cyto_label) == type(None) : raise ValueError("If cyto image is passed cyto label must be passed too.")
+
+    if dim == 3 and nuc_label.ndim == 2 :
+        nuc_label = np.repeat(
+            nuc_label[np.newaxis],
+            repeats= len(nuc_image),
+            axis=0
+        )
+    if type(cyto_label) != type(None) :
+        
+        if type(cyto_image) == type(None) : raise ValueError("If cyto label is passed cyto image must be passed too.")
+        
+        if dim == 3 and cyto_label.ndim == 2 :
+            cyto_label = np.repeat(
+                cyto_label[np.newaxis],
+                repeats= len(nuc_image),
+                axis=0
+            )
+
+    #Init Napari viewer
+    Viewer = napari.Viewer(ndisplay=2, title= 'Show segmentation', axis_labels=['z','y','x'] if dim == 3 else ['y', 'x'], show= False)
+    
+    # Adding channels
+    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.preserve_labels = True
+    
+    #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()])
+    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')
+        cyto_label_layer.preserve_labels = True
+    
+    #Launch Napari
+    Viewer.show(block=False)
+    napari.run()
+
+    new_nuc_label = Viewer.layers['nucleus_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
+
+def threshold_selection(
+        image : np.ndarray,
+        filtered_image : np.ndarray,
+        threshold_slider,
+        voxel_size : tuple,
+        ) :
+    
+    """
+    To view code for spot selection have a look at magicgui instance created with `detection._create_threshold_slider` which is then passed to this napari wrapper as 'threshold_slider' argument.
+    """
+    
+    Viewer = napari.Viewer(title= "Small fish - Threshold selector", ndisplay=2, show=True)
+    scale = compute_anisotropy_coef(voxel_size)
+    Viewer.add_image(
+        data= image,
+        contrast_limits= [image.min(), image.max()],
+        name= "raw signal",
+        colormap= 'green',
+        scale= scale,
+        blending= 'additive'
+    )
+    Viewer.add_image(
+        data= filtered_image,
+        contrast_limits= [filtered_image.min(), filtered_image.max()],
+        colormap= 'gray',
+        scale=scale,
+        blending='additive'
+    )
+
+    Viewer.window.add_dock_widget(threshold_slider, name='threshold_selector')
+    threshold_slider() #First occurence with auto or entered threshold.
+    
+    napari.run()
+
+    spots = Viewer.layers['single spots'].data.astype(int)
+    if len(spots) == 0 :
+        pass
+    else :
+        threshold = Viewer.layers['single spots'].properties.get('threshold')[0]
+
+    return spots, threshold

{small_fish_gui-1.4.0 → small_fish_gui-1.6.0}/src/small_fish_gui/pipeline/_preprocess.py

@@ -69,7 +69,7 @@ def map_channels(user_parameters) :
     try : 
         map = _auto_map_channels(is_3D_stack, is_time_stack, multichannel, image=image)
     except MappingError as e :
-        sg.popup("Automatic dimension mapping went wrong. Please indicate manually dimensions positions in the array.")
+        sg.popup("Automatic dimension mapping went wrong. Please indicate dimensions positions in the array.")
         map = _ask_channel_map(image.shape, is_3D_stack, is_time_stack, multichannel, preset_map= e.get_map())
 
     else :
@@ -125,14 +125,16 @@ def _auto_map_channels(is_3D_stack, is_time_stack, multichannel, image: np.ndarr
 def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map: dict= {}) :
     while True :
         relaunch = False
+        save_preset = preset_map.copy()
         x = preset_map.setdefault('x',0)
         y = preset_map.setdefault('y',0)
         z = preset_map.setdefault('z',0)
         c = preset_map.setdefault('c',0)
         t = preset_map.setdefault('t',0)
 
+
         layout = [
-            add_header("Dimensions mapping", [sg.Text("Image shape : {0}".format(shape))])
+            add_header("Dimensions mapping") + [sg.Text("Image shape : {0}".format(shape))]
         ]
         layout += [parameters_layout(['x','y'], default_values=[x,y])]
         if is_3D_stack : layout += [parameters_layout(['z'], default_values=[z])]
@@ -140,7 +142,7 @@ def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map
         if is_time_stack : layout += [parameters_layout(['t'], default_values=[t])]
 
         event, preset_map = prompt_with_help(layout,help= 'mapping', add_scrollbar=False)
-        if event == 'Cancel' : quit()
+        if event == 'Cancel' : return save_preset
 
         #Check integrity
         channels_values = np.array(list(preset_map.values()), dtype= int)
@@ -157,24 +159,26 @@ def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map
     return preset_map
 
 def _show_mapping(shape, map, is_3D_stack, is_time_stack, multichannel) :
-    layout = [
-        [sg.Text("Image shape : {0}".format(shape))],
-        [sg.Text('Dimensions mapping was set to :')],
-        [sg.Text('x : {0} \ny : {1} \nz : {2} \nc : {3} \nt : {4}'.format(
-            map['x'], map['y'], map.get('z'), map.get("c"), map.get('t')
-        ))],
-        [sg.Button('Change mapping')]
-    ]
-
-    event, values = prompt_with_help(layout, help='mapping', add_scrollbar=False)
-
-    if event == 'Ok' :
-        return map
-    elif event == 'Change mapping' or event == 'Cancel':
-        map = _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map=map)
-    else : raise AssertionError('Unforseen event')
+    while True : 
+        layout = [
+            [sg.Text("Image shape : {0}".format(shape))],
+            [sg.Text('Dimensions mapping was set to :')],
+            [sg.Text('x : {0} \ny : {1} \nz : {2} \nc : {3} \nt : {4}'.format(
+                map['x'], map['y'], map.get('z'), map.get("c"), map.get('t')
+            ))],
+            [sg.Button('Change mapping')]
+        ]
+
+        event, values = prompt_with_help(layout, help='mapping', add_scrollbar=False)
+
+        if event == 'Ok' :
+            return map
+        elif event == 'Change mapping':
+            map = _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map=map)
+        elif event == 'Cancel' : 
+            return None
+        else : raise AssertionError('Unforseen event')
 
-    return map
 
 def convert_parameters_types(values:dict) :
     """