small-fish-gui 1.3.4__py3-none-any.whl → 1.4.0__py3-none-any.whl

small_fish_gui/pipeline/_preprocess.py

@@ -67,7 +67,7 @@ def map_channels(user_parameters) :
     multichannel = user_parameters['multichannel']
 
     try : 
-        map = _auto_map_channels(image, is_3D_stack, is_time_stack, multichannel)
+        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.")
         map = _ask_channel_map(image.shape, is_3D_stack, is_time_stack, multichannel, preset_map= e.get_map())
@@ -77,8 +77,9 @@ def map_channels(user_parameters) :
 
     return map
 
-def _auto_map_channels(image: np.ndarray, is_3D_stack, is_time_stack, multichannel) :
-    shape = image.shape
+def _auto_map_channels(is_3D_stack, is_time_stack, multichannel, image: np.ndarray=None, shape=None) :
+    if type(shape) == type(None) :
+        shape = image.shape
     reducing_list = list(shape)
 
     #Set the biggest dimension to y
@@ -122,14 +123,13 @@ def _auto_map_channels(image: np.ndarray, is_3D_stack, is_time_stack, multichann
     return map
 
 def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map: dict= {}) :
-    map = preset_map
     while True :
         relaunch = False
-        x = map.setdefault('x',0)
-        y = map.setdefault('y',0)
-        z = map.setdefault('z',0)
-        c = map.setdefault('c',0)
-        t = map.setdefault('t',0)
+        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))])
@@ -139,12 +139,12 @@ def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map
         if multichannel : layout += [parameters_layout(['c'], default_values=[c])]
         if is_time_stack : layout += [parameters_layout(['t'], default_values=[t])]
 
-        event, map = prompt_with_help(layout,help= 'mapping')
+        event, preset_map = prompt_with_help(layout,help= 'mapping', add_scrollbar=False)
         if event == 'Cancel' : quit()
 
         #Check integrity
-        channels_values = np.array(list(map.values()), dtype= int)
-        total_channels = len(map)
+        channels_values = np.array(list(preset_map.values()), dtype= int)
+        total_channels = len(preset_map)
         unique_channel = len(np.unique(channels_values))
         if total_channels != unique_channel :
             sg.popup("{0} channel(s) are not uniquely mapped.".format(total_channels - unique_channel))
@@ -154,7 +154,7 @@ def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map
             relaunch= True
         if not relaunch : break
 
-    return map
+    return preset_map
 
 def _show_mapping(shape, map, is_3D_stack, is_time_stack, multichannel) :
     layout = [
@@ -166,7 +166,7 @@ def _show_mapping(shape, map, is_3D_stack, is_time_stack, multichannel) :
         [sg.Button('Change mapping')]
     ]
 
-    event, values = prompt_with_help(layout, help='mapping')
+    event, values = prompt_with_help(layout, help='mapping', add_scrollbar=False)
 
     if event == 'Ok' :
         return map
@@ -195,8 +195,8 @@ def convert_parameters_types(values:dict) :
         else : values[tuple_parameter] = tuple_values
 
     #Parameters
-    int_list = ['threshold', 'channel_to_compute', 'min number of spots', 'cluster size','nucleus channel signal']
-    float_list = ['time_step', 'alpha', 'beta', 'gamma', 'threshold penalty']
+    int_list = ['threshold', 'channel_to_compute', 'channel to compute', 'min number of spots', 'cluster size','nucleus channel signal']
+    float_list = ['alpha', 'beta', 'gamma', 'threshold penalty']
 
     for parameter in int_list :
         try :
@@ -214,7 +214,15 @@ def convert_parameters_types(values:dict) :
 
     return values
 
-def check_integrity(values: dict, do_dense_region_deconvolution, multichannel,segmentation_done, map, shape):
+def check_integrity(
+        values: dict, 
+        do_dense_region_deconvolution,
+        do_clustering, 
+        multichannel,
+        segmentation_done, 
+        map, 
+        shape
+        ):
     """
     Checks that parameters given in input by user are fit to be used for bigfish detection.
     """
@@ -234,10 +242,22 @@ def check_integrity(values: dict, do_dense_region_deconvolution, multichannel,se
             _warning_popup('No gamma found; image will not be denoised before deconvolution.')
             values['gamma'] = 0
 
+        if values['alpha'] > 1 or values['alpha'] < 0 :
+            raise ParameterInputError("alpha must be set between 0 and 1.")
+
+    if do_clustering :
+        if not isinstance(values['min number of spots'], (int)) :
+            raise ParameterInputError("Incorrect min spot number parameter.")
+        if not isinstance(values['cluster size'], (int)) :
+            raise ParameterInputError("Incorrect cluster size parameter.")
+
     #channel
     if multichannel :
         ch_len = shape[int(map['c'])]
-        if segmentation_done :
+
+        if type(segmentation_done) == type(None) :
+            pass
+        elif segmentation_done :
             try : nuc_signal_ch = int(values['nucleus channel signal'])
             except Exception :
                 raise ParameterInputError("Incorrect channel for nucleus signal measure.")
@@ -260,7 +280,6 @@ def check_integrity(values: dict, do_dense_region_deconvolution, multichannel,se
 
     return values
 
-
 def reorder_shape(shape, map) :
     x = [int(map['x']),]
     y = [int(map['y']),]
@@ -276,6 +295,40 @@ def reorder_shape(shape, map) :
 
     return new_shape
 
+def _check_segmentation_parameters(
+        user_parameters,
+        shape,
+        is_multichannel,
+) :
+
+    available_channels = list(range(len(shape)))
+    do_only_nuc = user_parameters['Segment only nuclei']
+    cyto_model_name = user_parameters['cyto_model_name']
+    cyto_size = user_parameters['cytoplasm diameter']
+    cytoplasm_channel = user_parameters['cytoplasm channel']
+    nucleus_model_name = user_parameters['nucleus_model_name']
+    nucleus_size = user_parameters['nucleus diameter']
+    nucleus_channel = user_parameters['nucleus channel']
+   
+
+    if type(cyto_model_name) != str  and not do_only_nuc:
+        raise ParameterInputError('Invalid cytoplasm model name.')
+    if cytoplasm_channel not in available_channels and not do_only_nuc and is_multichannel:
+        raise ParameterInputError('For given input image please select channel in {0}\ncytoplasm channel : {1}'.format(available_channels, cytoplasm_channel))
+
+    if type(cyto_size) not in [int, float] and not do_only_nuc:
+        raise ParameterInputError("Incorrect cytoplasm size.")
+
+    if type(nucleus_model_name) != str :
+        raise ParameterInputError('Invalid nucleus model name.')
+    
+    if nucleus_channel not in available_channels and is_multichannel:
+        raise ParameterInputError('For given input image please select channel in {0}\nnucleus channel : {1}'.format(available_channels, nucleus_channel))
+    
+    if type(nucleus_size) not in [int, float] :
+        raise ParameterInputError("Incorrect nucleus size.")
+
+
 def clean_unused_parameters_cache(user_parameters: dict) :
     """
     Clean unused parameters that were set to None in previous run.

small_fish_gui/pipeline/_segmentation.py

@@ -170,7 +170,7 @@ def launch_segmentation(image: np.ndarray, user_parameters: dict) :
                 [sg.Button("Yes"), sg.Button("No")]
             ]
             
-            event, values = prompt(layout=layout, add_ok_cancel=False)
+            event, values = prompt(layout=layout, add_ok_cancel=False, add_scrollbar=False)
             if event == "No" :
                 continue
 
@@ -351,3 +351,39 @@ def remove_disjoint(image):
         image_cleaned = image_cleaned.astype(bool)
 
     return image_cleaned
+
+def plot_segmentation(
+        cyto_image : np.ndarray, 
+        cyto_label : np.ndarray, 
+        nuc_image : np.ndarray, 
+        nuc_label : np.ndarray,
+        path :str, 
+        do_only_nuc=False
+        ) :
+
+    if nuc_image.ndim == 3 :
+        nuc_image = np.max(nuc_image,axis=0)
+    
+    plot.plot_segmentation_boundary(
+        image=nuc_image,
+        nuc_label= nuc_label,
+        boundary_size= 3,
+        contrast=True,
+        path_output=path + "_nuclei_segmentation.png",
+        show=False,
+    )
+
+
+    if not do_only_nuc :
+        if cyto_image.ndim == 3 :
+            cyto_image = np.max(cyto_image,axis=0)
+    
+        plot.plot_segmentation_boundary(
+            image=cyto_image,
+            cell_label= cyto_label,
+            nuc_label= nuc_label,
+            boundary_size= 3,
+            contrast=True,
+            path_output=path + "_cytoplasm_segmentation.png",
+            show=False,
+        )

small_fish_gui/pipeline/detection.py

@@ -8,6 +8,7 @@ from ._signaltonoise import compute_snr_spots
 from ._napari_wrapper import correct_spots, _update_clusters, threshold_selection
 from ..gui import add_default_loading
 from ..gui import detection_parameters_promt, input_image_prompt
+from ..utils import compute_anisotropy_coef
 from .spots import compute_Spots
 from magicgui import magicgui
 from napari.layers import Image, Points
@@ -25,6 +26,7 @@ import bigfish.classification as classification
 from bigfish.detection.spot_detection import get_object_radius_pixel
 from types import GeneratorType
 from skimage.measure import regionprops
+from scipy.ndimage import binary_dilation
 
 
 def ask_input_parameters(ask_for_segmentation=True) :
@@ -281,7 +283,15 @@ def initiate_detection(user_parameters, segmentation_done, map, shape) :
         if type(user_parameters) == type(None) : return user_parameters
         try :
             user_parameters = convert_parameters_types(user_parameters)
-            user_parameters = check_integrity(user_parameters, do_dense_region_deconvolution, is_multichannel, segmentation_done, map, shape)
+            user_parameters = check_integrity(
+                user_parameters, 
+                do_dense_region_deconvolution,
+                do_clustering, 
+                is_multichannel, 
+                segmentation_done, 
+                map, 
+                shape
+                )
         except ParameterInputError as error:
             sg.popup(error)
         else :
@@ -591,7 +601,8 @@ def launch_detection(
         other_image,
         user_parameters,
         cell_label= None,
-        nucleus_label = None
+        nucleus_label = None,
+        hide_loading=False,
         ) :
     """
     Main call for features computation :
@@ -617,18 +628,18 @@ def launch_detection(
     do_dense_region_deconvolution = user_parameters['Dense regions deconvolution']
     do_clustering = user_parameters['Cluster computation']
 
-    spots, threshold  = _launch_detection(image, user_parameters)
+    spots, threshold  = _launch_detection(image, user_parameters, hide_loading = hide_loading)
         
     if do_dense_region_deconvolution : 
-        spots = launch_dense_region_deconvolution(image, spots, user_parameters)
+        spots = launch_dense_region_deconvolution(image, spots, user_parameters, hide_loading = hide_loading)
         
     if do_clustering : 
-        clusters = launch_clustering(spots, user_parameters) #012 are coordinates #3 is number of spots per cluster, #4 is cluster index
+        clusters = launch_clustering(spots, user_parameters, hide_loading = hide_loading) #012 are coordinates #3 is number of spots per cluster, #4 is cluster index
         clusters = _update_clusters(clusters, spots, voxel_size=user_parameters['voxel_size'], cluster_size=user_parameters['cluster size'], min_spot_number= user_parameters['min number of spots'], shape=image.shape)
 
     else : clusters = None
 
-    spots, post_detection_dict = launch_post_detection(image, spots, user_parameters)
+    spots, post_detection_dict = launch_post_detection(image, spots, user_parameters, hide_loading = hide_loading)
     user_parameters['threshold'] = threshold
 
     if user_parameters['Napari correction'] :
@@ -766,9 +777,11 @@ def _create_threshold_slider(
             threshold=threshold
         )[0]
 
+        scale = compute_anisotropy_coef(voxel_size)
+
         layer_args = {
             'size': 5, 
-            'scale' : voxel_size, 
+            'scale' : scale, 
             'face_color' : 'transparent', 
             'edge_color' : 'blue', 
             'symbol' : 'ring', 
@@ -822,4 +835,55 @@ def _local_maxima_mask(
             ndim=ndim)
     mask_local_max = detection.local_maximum_detection(image_filtered, minimum_distance)
     
-    return mask_local_max.astype(bool)
+    return mask_local_max.astype(bool)
+
+def output_spot_tiffvisual(channel,spots_list, path_output, dot_size = 3, rescale = True):
+    
+    """
+    Outputs a tiff image with one channel being {channel} and the other a mask containing dots where sports are located.
+    
+    Parameters
+    ----------
+        channel : np.ndarray
+            3D monochannel image
+        spots : list[np.ndarray] or np.ndarray
+            Spots arrays are ndarray where each element corresponds is a tuple(z,y,x) corresponding to 3D coordinate of a spot
+            To plot different spots on different channels a list of spots ndarray can be passed. 
+        path_output : str
+        dot_size : int
+            in pixels
+    """
+    
+    stack.check_parameter(channel = (np.ndarray), spots_list= (list, np.ndarray), path_output = (str), dot_size = (int))
+    stack.check_array(channel, ndim= [2,3])
+    if isinstance(spots_list, np.ndarray) : spots_list = [spots_list]
+
+    if channel.ndim == 3 : 
+        channel = stack.maximum_projection(channel)
+
+    im = np.zeros([1 + len(spots_list)] + list(channel.shape))
+    im[0,:,:] = channel
+
+    for level in range(len(spots_list)) :
+        if len(spots_list[level]) == 0 : continue
+        else :
+            spots_mask = np.zeros_like(channel)
+            
+            #Unpacking spots
+            if len(spots_list[level][0]) == 2 :
+                Y,X = zip(*spots_list[level])
+            elif len(spots_list[level][0]) == 3 :
+                Z,Y,X = zip(*spots_list[level])
+                del Z
+            else :
+                Z,Y,X,*_ = zip(*spots_list[level])
+                del Z,_
+            
+            #Reconstructing signal
+            spots_mask[Y,X] = 1
+            if dot_size > 1 : spots_mask = binary_dilation(spots_mask, iterations= dot_size-1)
+            spots_mask = stack.rescale(np.array(spots_mask, dtype = channel.dtype))
+            im[level + 1] = spots_mask
+
+    if rescale : channel = stack.rescale(channel, channel_to_stretch= 0)
+    stack.save_image(im, path_output, extension= 'tif')

small_fish_gui/pipeline/main.py

@@ -4,6 +4,7 @@ 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.
@@ -24,7 +25,6 @@ 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 +74,12 @@ 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/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-1.3.4.dist-info → small_fish_gui-1.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.3.4
+Version: 1.4.0
 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.dist-info/RECORD

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small_fish_gui/gui/test.py

@@ -1,4 +0,0 @@
-import PySimpleGUI as sg
-import small_fish.gui.prompts as p
-
-p.hub_prompt([{},{},{"cell_number" : 100, "spot_number" : 1000},{},{},{'cell_number' : 10},{}])

small_fish_gui-1.3.4.dist-info/RECORD

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