small-fish-gui 1.3.5__py3-none-any.whl → 1.5.0__py3-none-any.whl

small_fish_gui/pipeline/main.py

@@ -1,12 +1,16 @@
-#### New version for main.py
+"""
+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 ._preprocess import clean_unused_parameters_cache
+from ..batch import batch_promp
 
 #'Global' parameters
-user_parameters = dict() # Very important object containg all choice from user that will influence the behavior of the main loop.
+user_parameters = dict() # Very important instance containg all choice from user that will influence the behavior of the actions loops.
 acquisition_id = -1
 result_df = pd.DataFrame()
 cell_result_df = pd.DataFrame()
@@ -24,7 +28,6 @@ while True : #Break this loop to close small_fish
 
         if event == 'Add detection' :
             user_parameters = clean_unused_parameters_cache(user_parameters)
-            
 
             new_result_df, new_cell_result_df, acquisition_id, user_parameters, segmentation_done, cytoplasm_label, nucleus_label =  add_detection(
                 user_parameters=user_parameters,
@@ -74,8 +77,12 @@ while True : #Break this loop to close small_fish
             result_df, cell_result_df, coloc_df = delete_acquisitions(selected_acquisitions, result_df, cell_result_df, coloc_df)
 
         elif event == "Batch detection" :
-        #TODO
-            pass
+            result_df, cell_result_df, acquisition_id, user_parameters, segmentation_done, cytoplasm_label,nucleus_label = batch_promp(
+                result_df,
+                cell_result_df,
+                acquisition_id=acquisition_id,
+                preset=user_parameters,
+            )
         
         else :
             break

small_fish_gui/pipeline/utils.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+from math import ceil
+from itertools import zip_longest
+from skimage.measure import regionprops_table
+
+
+def from_label_get_centeroidscoords(label: np.ndarray):
+    """
+    Returns
+    --------
+      centroid : dict{"label": list, "centroid-n": list} 
+        n should be replace with 1,2.. according to the axe you wish to access."""
+
+    centroid = regionprops_table(label, properties= ["label","centroid"])
+    return centroid

small_fish_gui/utils.py

@@ -1,4 +1,5 @@
 import inspect
+import datetime as dt
 
 def check_parameter(**kwargs):
     """Check dtype of the function's parameters.
@@ -52,4 +53,8 @@ def compute_anisotropy_coef(voxel_size) :
         return (z_anisotropy, xy_anisotropy, 1)
 
     else :
-        return (voxel_size[0] / voxel_size[1], 1)
+        return (voxel_size[0] / voxel_size[1], 1)
+    
+
+def get_datetime():
+    return dt.datetime.now().strftime("%Y%m%d %H-%M-%S")

{small_fish_gui-1.3.5.dist-info → small_fish_gui-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.3.5
+Version: 1.5.0
 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.dist-info/RECORD

@@ -0,0 +1,52 @@
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small_fish_gui/gui/batch.py

@@ -1,312 +0,0 @@
-import os
-import numpy as np
-import PySimpleGUI as sg
-import bigfish.stack as stack
-import czifile as czi
-
-from .layout import _segmentation_layout, _detection_layout, _input_parameters_layout, _ask_channel_map_layout
-
-
-from time import sleep
-
-def get_images(filename:str) :
-    """returns filename if is image else return None"""
-
-    supported_types = ('.tiff', '.tif', '.png', '.czi')
-    if filename.endswith(supported_types) : 
-        return [filename]
-    else :
-        return None
-
-
-def get_files(path) :
-
-    filelist = os.listdir(path)
-    filelist = list(map(get_images,filelist))
-
-    while None in filelist : filelist.remove(None)
-
-    return filelist
-
-def extract_files(filenames: list) :
-    return sum(filenames,[])
-
-def check_file(filename:str) :
-
-    if filename.endswith('.czi') :
-        image = czi.imread(filename)
-    else :
-        image = stack.read_image(filename)
-
-    image = np.squeeze(image)
-
-    return image.shape
-
-def sanity_check(
-        filename_list: list, 
-        batch_folder : str,
-        window : sg.Window, 
-        progress_bar: sg.ProgressBar,
-        ) :
-    
-    filenumber = len(filename_list)
-    if filenumber == 0 :
-        print("No file to check")
-        progress_bar.update(current_count= 0, bar_color=('gray','gray'))
-        return None
-    else :
-        print("{0} files to check".format(filenumber))
-        progress_bar.update(current_count=0, max= filenumber)
-        ref_shape = check_file(batch_folder + '/' + filename_list[0])
-
-        print("Starting sanity check. This could take some time...")
-        for i, file in enumerate(filename_list) :
-            progress_bar.update(current_count= i+1, bar_color=('green','gray'))
-            shape = check_file(batch_folder + '/' + file)
-
-            if len(shape) != len(ref_shape) : #then dimension missmatch
-                print("Different number of dimensions found : {0}, {1}".format(len(ref_shape), len(shape)))
-                progress_bar.update(current_count=filenumber, bar_color=('red','black'))
-                window= window.refresh()
-                break
-
-            window= window.refresh()
-
-        print("Sanity check completed.")
-        return None if len(shape) != len(ref_shape) else shape
-
-
-def get_elmt_from_key(Tab_elmt:sg.Tab, key) -> sg.Element:
-    elmt_list = sum(Tab_elmt.Rows,[])
-    for elmt in elmt_list :
-        if elmt.Key == key : return elmt
-    raise KeyError("{0} key not found amongst {1}.".format(key, [elmt.Key for elmt in elmt_list]))
-
-def update_detection_tab(
-        tab_elmt:sg.Tab, 
-        is_multichannel, 
-        is_3D, 
-        do_dense_region_deconvolution,
-        do_clustering
-        ) :
-    
-    #Acess elements
-    ##Detection
-    channel_to_compute = get_elmt_from_key(tab_elmt, key= 'channel to compute')
-    voxel_size_z = get_elmt_from_key(tab_elmt, key= 'voxel_size_z')
-    spot_size_z = get_elmt_from_key(tab_elmt, key= 'spot_size_z')
-    log_kernel_size_z = get_elmt_from_key(tab_elmt, key= 'log_kernel_size_z')
-    minimum_distance_z = get_elmt_from_key(tab_elmt, key= 'minimum_distance_z')
-
-    ##Dense regions deconvolution
-    alpha = get_elmt_from_key(tab_elmt, key= 'alpha')
-    beta = get_elmt_from_key(tab_elmt, key= 'beta')
-    gamma = get_elmt_from_key(tab_elmt, key= 'gamma')
-    deconvolution_kernel_z = get_elmt_from_key(tab_elmt, key= 'deconvolution_kernel_z')
-    cluster_size = get_elmt_from_key(tab_elmt, key= 'cluster size')
-    min_number_of_spot = get_elmt_from_key(tab_elmt, key= 'min number of spots')
-    nucleus_channel_signal = get_elmt_from_key(tab_elmt, key= 'nucleus channel signal')
-    interactive_threshold_selector = get_elmt_from_key(tab_elmt, key= 'Interactive threshold selector')
-
-    update_dict={
-        'is_3D' : is_3D,
-        'is_multichannel' : is_multichannel,
-        'do_dense_region_deconvolution' : do_dense_region_deconvolution,
-        'do_clustering' : do_clustering,
-        'always_hidden' : False
-    }
-
-    list_dict={
-        'is_3D' : [voxel_size_z, spot_size_z, log_kernel_size_z, minimum_distance_z, deconvolution_kernel_z],
-        'is_multichannel' : [channel_to_compute, nucleus_channel_signal],
-        'do_dense_region_deconvolution' : [alpha,beta,gamma],
-        'do_clustering' : [cluster_size, min_number_of_spot],
-        'always_hidden' : [interactive_threshold_selector]
-        
-    }
-
-    for key, enabled in update_dict.items() :
-        for elmt in list_dict.get(key) :
-            elmt.update(disabled=not enabled)
-    
-
-
-def update_segmentation_tab(tab_elmt : sg.Tab, do_segmentation, is_multichannel) : #TODO
-    
-    #Access elements
-    cytoplasm_channel_elmt = get_elmt_from_key(tab_elmt, key= 'cytoplasm channel')
-    nucleus_channel_elmt = get_elmt_from_key(tab_elmt, key= 'nucleus channel')
-    
-    #Update values
-    tab_elmt.update(visible=do_segmentation)
-    cytoplasm_channel_elmt.update(disabled = not is_multichannel)
-    nucleus_channel_elmt.update(disabled = not is_multichannel)
-
-def update_map_tab() :
-    #TODO
-    pass
-
-def batch_promp() :
-
-    files_values = [[]]
-
-
-    #LOAD FILES
-    files_table = sg.Table(values=files_values, headings=['Filenames'], col_widths=100, max_col_width= 200, def_col_width=100, num_rows= 10, auto_size_columns=False)
-
-    #Start&Stop
-    start_button =sg.Button('Start', button_color= 'green', disabled= True)
-    stop_button = sg.Button('Cancel', button_color= 'red')
-
-    #DIMENSION SANITY
-    sanity_progress = sg.ProgressBar(10, size_px=(500,10))
-    sanity_check_button = sg.Button(
-        'Check', 
-        tooltip= "Will check that all files loaded have the same dimension number and that small fish is able to open them.", 
-        pad=(10,0))
-    sanity_header = sg.Text("Dimension sanity", font=('bold',15), pad=(0,10))
-    dimension_number_text = sg.Text("Dimension number : unknown")
-
-    #Input tab
-    input_layout = _input_parameters_layout(
-        ask_for_segmentation=True,
-        is_3D_stack_preset=False,
-        time_stack_preset=False,
-        multichannel_preset=False,
-        do_dense_regions_deconvolution_preset=False,
-        do_clustering_preset=False,
-        do_Napari_correction=False,
-        do_segmentation_preset=False,
-    )
-    input_layout += [[sg.Button('Ok')]]
-    input_tab = sg.Tab("Input", input_layout)
-
-    #Maptab
-    map_layout = _ask_channel_map_layout(
-        shape=(0,1,2,3,4),
-        is_3D_stack=True,
-        is_time_stack=True,
-        multichannel=True,
-    )
-    last_shape_read = sg.Text("Last shape read : None")
-    auto_map = sg.Button("auto-map", disabled=True, pad=(10,0))
-    map_layout += [[last_shape_read, auto_map]]
-    map_tab = sg.Tab("Map", map_layout)
-
-    #Segmentation tab
-    segmentation_layout = _segmentation_layout(multichannel=True, cytoplasm_model_preset='cyto3')
-    segmentation_tab = sg.Tab("Segmentation", segmentation_layout, visible=False)
-
-    #Detection tab
-    detection_layout = _detection_layout(
-        is_3D_stack=True,
-        is_multichannel=True,
-        do_clustering=True,
-        do_dense_region_deconvolution=True,
-        do_segmentation=True,
-    )
-
-
-    detection_tab = sg.Tab("Detection", detection_layout)
-    
-        
-
-    #TABS
-    _tab_group = sg.TabGroup([[input_tab, map_tab, segmentation_tab, detection_tab]], enable_events=True)
-    tab_group = sg.Column( #Allow the tab to be scrollable
-        [[_tab_group]],
-        scrollable=True,
-        vertical_scroll_only=True,
-        pad=(150,5)
-        )
-    tab_dict= {
-        "Input" : input_tab,
-        "Segmentation" : segmentation_tab,
-        "Detection" : detection_tab,
-        "Map" : map_tab,
-    }
-
-    layout = [
-        [sg.Text("Batch Processing", font=('bold',20), pad=((300,0),(0,2)))],
-        [sg.Text("Select a folder : "), sg.FolderBrowse(initial_folder=os.getcwd(), key='Batch_folder'), sg.Button('Load')],
-        [files_table],
-        [sanity_header, sanity_check_button, sanity_progress],
-        [dimension_number_text],
-        [tab_group],
-        [sg.Output(size=(100,10), pad=(30,10))],
-        [start_button, stop_button],
-    ]
-
-    window = sg.Window("small fish", layout=layout, size= (800,800), auto_size_buttons=True, auto_size_text=True)
-    loop = 0
-    timeout = 1
-    while True :
-        loop +=1
-        window = window.refresh()
-        event, values = window.read(timeout=timeout)
-        
-        #Welcome message
-        if loop == 1 : 
-            timeout = None
-            print("Welcome to small fish batch analysis. Please start by loading some files and setting parameters.")
-        
-        batch_folder = values.get('Batch_folder')
-        is_multichanel = values.get('multichannel')
-        is_3D = values.get('3D stack')
-        do_segmentation = values.get('Segmentation')
-        do_dense_regions_deconvolution = values.get('Dense regions deconvolution')
-        do_clustering = values.get('Cluster computation')
-
-        if type(batch_folder) != type(None)  and event == 'Load':
-            if not os.path.isdir(batch_folder) :
-                print("Can't open {0}".format(batch_folder))
-            else :
-                files_values = get_files(batch_folder)
-                files_table.update(values=files_values)
-
-        elif event == 'Check' :
-            filename_list = extract_files(files_values)
-            last_shape = sanity_check(
-                filename_list=filename_list,
-                batch_folder=batch_folder,
-                window=window,
-                progress_bar=sanity_progress
-            )
-            if isinstance(last_shape,(tuple,list)) :
-                dim_number = len(last_shape)
-                dimension_number_text.update("Dimension number : {0}".format(dim_number))
-                auto_map.update(disabled=False)
-            else :
-                dimension_number_text.update("Dimension number : unknown")
-                auto_map.update(disabled=True)
-
-            last_shape_read.update("Last shape read : {0}".format(last_shape))
-           
-        
-        elif event == _tab_group.key or event == 'Ok': #Tab switch in parameters
-            update_segmentation_tab(
-                tab_elmt=tab_dict.get("Segmentation"),
-                do_segmentation=do_segmentation,
-                is_multichannel=is_multichanel,
-            )
-
-            update_detection_tab(
-                tab_elmt=tab_dict.get("Detection"),
-                is_multichannel=is_multichanel,
-                is_3D=is_3D,
-                do_dense_region_deconvolution=do_dense_regions_deconvolution,
-                do_clustering=do_clustering,
-            )
-
-        elif event == 'auto-map' :
-            #TODO
-            pass
-
-        # elif event == 'apply' (map) #TODO
-
-        # elif event == 'check parameters' -> un/lock start #TODO
-            
-        elif event == "Cancel" :
-            print(values)
-        elif event == None :
-            quit()

small_fish_gui/gui/test.py

@@ -1,5 +0,0 @@
-import PySimpleGUI as sg
-import small_fish_gui.gui.batch as prompt
-
-prompt.batch_promp()
-print('end')

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