small-fish-gui 2.0.2__py3-none-any.whl → 2.1.0__py3-none-any.whl

small_fish_gui/gui/layout.py

@@ -1,15 +1,18 @@
 import FreeSimpleGUI as sg
 import os
+import numpy as np
 import cellpose.models as models
-import small_fish_gui.default_values as default
 from typing import Optional, Union
 
 from cellpose.core import use_gpu
-from .tooltips import FLOW_THRESHOLD_TOOLTIP,CELLPROB_TOOLTIP
+from .tooltips import FLOW_THRESHOLD_TOOLTIP,CELLPROB_TOOLTIP, MIN_SIZE_TOOLTIP
 from ..hints import pipeline_parameters
 from ..utils import check_parameter
+from ..interface import SettingsDict, get_default_settings, get_settings
 
 
+settings = get_settings()
+
 def add_header(header_text) :
     """Returns [elmnt] not layout"""
     header = [sg.Text('\n{0}'.format(header_text), size= (len(header_text),3), font= 'bold 15')]
@@ -66,9 +69,14 @@ def parameters_layout(
              ] for parameter, option in zip(parameters, opt)
         ]
     
-    if type(unit) == str :
+    if isinstance(unit, str):
         for line_id, line in enumerate(layout) :
             layout[line_id] += [sg.Text('{0}'.format(unit))]
+    elif isinstance(unit, list) :
+        if len(unit) != len(parameters) : raise ValueError(f"unit list and parameters must have same length : {len(unit)} , {len(parameters)}")
+
+        for line_id, unit_txt in zip(range(len(parameters)), unit) :
+            layout[line_id] += [sg.Text('{0}'.format(unit_txt))]
     
     if isinstance(header, str) :
         layout = [add_header(header)] + layout
@@ -103,13 +111,14 @@ def tuple_layout(opt=None, default_dict={}, unit:dict={}, names : dict = {}, **t
 
     return layout
 
-def path_layout(keys= [],look_for_dir = False, header=None, preset=os.getcwd()) :
+def path_layout(keys= [],look_for_dir = False, header=None, preset=settings.working_directory) :
     """
     If not look for dir then looks for file.
     """
     if len(keys) == 0 : return []
     check_parameter(keys= list, header = (str, type(None)))
     for key in keys : check_parameter(key = str)
+    
     if look_for_dir : Browse = sg.FolderBrowse
     else : Browse = sg.FileBrowse
 
@@ -185,105 +194,197 @@ def radio_layout(values, header=None, key=None) :
     return layout
 
 def _segmentation_layout(
-        multichannel : bool,
+        is_multichannel : bool,
         is_3D_stack : bool,
-        cytoplasm_model_preset= default.CYTO_MODEL, 
-        nucleus_model_preset= default.NUC_MODEL, 
-        cytoplasm_channel_preset=default.CHANNEL, 
-        nucleus_channel_preset=default.NUC_CHANNEL, 
-        other_nucleus_image_preset = None,
-        cyto_diameter_preset=default.CYTO_DIAMETER, 
-        nucleus_diameter_preset= default.NUC_DIAMETER, 
-        show_segmentation_preset= default.SHOW_SEGMENTATION,
-        save_segmentation_visual_preset = default.SAVE_SEGMENTATION_VISUAL, 
-        segment_only_nuclei_preset=default.SEGMENT_ONLY_NUCLEI, 
-        saving_path_preset=default.VISUAL_PATH, 
-        filename_preset='cell_segmentation.png',
-        cytoplasm_segmentation_3D = default.DO_3D_SEMGENTATION,
-        nucleus_segmentation_3D = default.DO_3D_SEMGENTATION,
-        cellprob_threshold = default.CELLPROB_THRESHOD,
-        flow_threshold = default.FLOW_THRESHOLD,
-        anisotropy= default.ANISOTROPY,
+        cytoplasm_model,
+        nucleus_model,
+        cytoplasm_channel,
+        nucleus_channel,
+        other_nucleus_image,
+        cytoplasm_diameter,
+        nucleus_diameter,
+        show_segmentation,
+        save_segmentation_visuals, 
+        segment_only_nuclei,
+        saving_path,
+        filename,
+        cytoplasm_segmentation_3D ,
+        nucleus_segmentation_3D ,
+        cellprob_threshold ,
+        flow_threshold ,
+        anisotropy,
+        cytoplasm_min_size : int,
+        nucleus_min_size : int,
+        reordered_shape : tuple,
+        **kwargs
         ) :
     
     USE_GPU = use_gpu()
-
-    models_list = models.get_user_models() + models.MODEL_NAMES
-    if len(models_list) == 0 : models_list = ['no model found']
+    event_dict = dict()
     
     #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("Cell Segmentation", font="bold 20", pad=(0,20))]]
+    layout += [[sg.Text("GPU is currently "), sg.Text('ON', text_color= 'green') if USE_GPU else sg.Text('OFF', text_color= 'red')]]
+    layout += bool_layout(['Interactive segmentation'],keys=['show_segmentation'], preset= show_segmentation)
+    
+    segment_only_nuclei_checkbox = sg.Checkbox("Segment only nuclei", default=segment_only_nuclei, key= "segment_only_nuclei", enable_events=True) 
+    layout += [[segment_only_nuclei_checkbox]]
+    event_dict['segment_only_nuclei'] = segment_only_nuclei_checkbox
     
-    #cytoplasm parameters
-    layout += [
-        add_header("Cytoplasm Segmentation"),
-        [sg.Text("Choose parameters for cytoplasm segmentation: \n")],
-                        ]
-                        
-    if is_3D_stack : layout += bool_layout(['3D segmentation'], preset=[cytoplasm_segmentation_3D], keys=['cytoplasm_segmentation_3D'],)
-    if multichannel : layout += parameters_layout(['Cytoplasm channel'],default_values= [cytoplasm_channel_preset], keys = ["cytoplasm_channel"])
-
-    layout += [[sg.Text("Cellpose model : ")] + combo_elmt(models_list, key='cyto_model_name', default_value= cytoplasm_model_preset)]
-    layout += parameters_layout(['Cytoplasm diameter'], unit= "px", default_values= [cyto_diameter_preset], keys=['cytoplasm_diameter'])
-    layout += parameters_layout(
-        ["Flow threshold", "Cellprob threshold"], 
-        default_values=[flow_threshold, cellprob_threshold], 
-        keys=["flow_threshold_cyto","cellprob_threshold_cyto"],
-        tooltips= [FLOW_THRESHOLD_TOOLTIP, CELLPROB_TOOLTIP]
-        )
-
     #Nucleus parameters
-    layout += [
-            add_header("Nuclei segmentation"),
-            [sg.Text("Choose parameters for nuclei segmentation: \n")],
+    nucleus_key = "nucleus"
+    layout += [[sg.Text("Nucleus parameters", font="bold 15", pad=(0,10))]]
+    nucleus_parameters_col, nucleus_event_dict = _segmentate_object_layout(
+        reordered_shape = reordered_shape,
+        anisotropy=anisotropy,
+        cellprob_threshold=cellprob_threshold,
+        channel=nucleus_channel,
+        diameter=nucleus_diameter,
+        flow_threshold=flow_threshold,
+        is_3D_stack=is_3D_stack,
+        model=nucleus_model,
+        is_multichannel=is_multichannel,
+        object_key=nucleus_key,
+        segmentation_3D=nucleus_segmentation_3D,
+        min_size=nucleus_min_size
+    )
+    layout += path_layout(keys=["other_nucleus_image"], look_for_dir=False, preset=other_nucleus_image)
+    layout += [[nucleus_parameters_col]]
+    event_dict.update(nucleus_event_dict)
+    event_dict[nucleus_key + "_column"] = nucleus_parameters_col
+
+
+    #Cytoplasm parameters
+    layout += [[sg.Text("Cytoplasm parameters", font="bold 15", pad=(0,10))]]
+    cytoplasm_key = "cytoplasm"
+    cytoplasm_parameters_col, cytoplasm_event_dict = _segmentate_object_layout(
+        reordered_shape = reordered_shape,
+        anisotropy=anisotropy,
+        cellprob_threshold=cellprob_threshold,
+        channel=cytoplasm_channel,
+        diameter=cytoplasm_diameter,
+        flow_threshold=flow_threshold,
+        is_3D_stack=is_3D_stack,
+        model=cytoplasm_model,
+        is_multichannel=is_multichannel,
+        object_key=cytoplasm_key,
+        segmentation_3D=cytoplasm_segmentation_3D,
+        min_size=cytoplasm_min_size
+    )
+    layout += [[cytoplasm_parameters_col]]
+    event_dict.update(cytoplasm_event_dict)
+    event_dict[cytoplasm_key + "_column"] = cytoplasm_parameters_col
+
+    #Control plots
+    layout += [[sg.Text("Control plots", font="bold 15", pad=(0,10))]]
+    layout += bool_layout(['Save png control'], preset= save_segmentation_visuals, keys=['save_segmentation_visuals'])
+    layout += path_layout(keys=['seg_control_saving_path'], look_for_dir=True, preset=saving_path)
+    layout += parameters_layout(['Filename'], default_values=[filename], size= 25, keys=['filename'])
+
+    return layout, event_dict
+
+def _segmentate_object_layout(
+    reordered_shape : tuple | None,
+    object_key : str,     
+    is_multichannel : bool,
+    is_3D_stack : bool,
+    model : str,
+    channel : int,
+    diameter : int,
+    segmentation_3D : bool ,
+    cellprob_threshold : float ,
+    flow_threshold : float,
+    anisotropy : float,
+    min_size : int,
+    **kwargs
+    ) -> sg.Column :
+
+    models_list = models.get_user_models() + models.MODEL_NAMES
+    if len(models_list) == 0 : models_list = ['no model found']
+
+    key_2D = object_key + "_radio_2D"
+    options_2D = list()
+    key_3D = object_key + "_radio_3D"
+    options_3D = list()
+    layout = []
+
+    radio_2D_seg = sg.Radio("2D segmentation", group_id=object_key+"_seg_dim", default=not segmentation_3D, visible = True, enable_events=True, key=key_2D)
+    radio_max_proj = sg.Radio("max proj", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key= object_key+"_max_proj")
+    radio_mean_proj = sg.Radio("mean proj", group_id=object_key+"_2D_proj", default=True, disabled= segmentation_3D, key = object_key + "_mean_proj")
+    radio_slice_proj = sg.Radio("select slice", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key=object_key + "_select_slice")
+    radio_3D_seg = sg.Radio("3D segmentation", group_id=object_key+"_seg_dim", default=segmentation_3D, visible = True, enable_events=True, key= key_3D)
+    anisotropy = sg.Input(default_text = 1, key = object_key + "_anisotropy",size=5, disabled=not segmentation_3D)
+
+    if is_3D_stack :        
+        slice_number = reordered_shape[0 + is_multichannel] if not reordered_shape is None else 999
+        int_slice_proj = sg.Spin(list(range(slice_number)), size= (5,1), disabled= segmentation_3D, key=object_key+"_selected_slice")
+
+        options_2D += [
+            radio_max_proj, 
+            radio_mean_proj, 
+            radio_slice_proj, 
+            int_slice_proj
+            ]
+
+        layout += [
+                [radio_2D_seg],
+                [sg.Column([[radio_max_proj, radio_mean_proj, radio_slice_proj, int_slice_proj]], pad= (15,0,0,5))]
                 ]
-    
-    layout += path_layout(['other_nucleus_image'], preset=other_nucleus_image_preset)
-    if is_3D_stack : layout += bool_layout(['3D segmentation'], preset=[nucleus_segmentation_3D], keys=['nucleus_segmentation_3D'],)
-    if multichannel : layout += parameters_layout(['nucleus_channel'], default_values= [nucleus_channel_preset])
-    layout += bool_layout(["Segment only nuclei"], preset=segment_only_nuclei_preset, keys=["segment_only_nuclei"])
-    
-    layout += [[sg.Text("Cellpose model : ")] + combo_elmt(models_list, key='nucleus_model_name', default_value= nucleus_model_preset)]
-    layout += parameters_layout(['Nucleus diameter'],unit= "px", default_values= [nucleus_diameter_preset], keys=['nucleus_diameter'])
+
+
+        layout += [
+            [radio_3D_seg],
+            [sg.Column([[sg.Text("anisotropy"), anisotropy]], pad=(15,0,0,5))]
+            ]  
+        
+        options_3D += [
+            anisotropy
+        ]
+
+    if is_multichannel : 
+        channel_elmt = sg.Input(channel, key=object_key + "_channel", size=5)
+        layout += [[sg.Text(f'{object_key.capitalize()} channel'), channel_elmt]]
+
+    layout += [[sg.Text("Cellpose model : ")] + combo_elmt(models_list, key=object_key +'_model_name', default_value= model)]
+    layout += parameters_layout([f'{object_key.capitalize()} diameter'], unit= "px", default_values= [diameter], keys=[object_key+'_diameter'])
     layout += parameters_layout(
-        ["Flow threshold", "Cellprob threshold"], 
-        default_values=[flow_threshold, cellprob_threshold], 
-        keys=["flow_threshold_nuc","cellprob_threshold_nuc"],
-        tooltips= [FLOW_THRESHOLD_TOOLTIP, CELLPROB_TOOLTIP]
-        )
-    if is_3D_stack : layout += parameters_layout(
-        ['anisotropy'], 
-        header = "Model parameters",
-        default_values = [anisotropy]
+        ["Flow threshold", "Cellprob threshold", "Min. size"],
+        unit=["","","px"], 
+        default_values=[flow_threshold, cellprob_threshold, min_size], 
+        keys=[object_key + "_flow_threshold",object_key + "_cellprob_threshold", object_key + "_min_size"],
+        tooltips= [FLOW_THRESHOLD_TOOLTIP, CELLPROB_TOOLTIP, MIN_SIZE_TOOLTIP]
         )
 
-    #Control plots
-    layout += bool_layout(['Show_segmentation'],keys=['show_segmentation'], header= 'Segmentation plots', preset= show_segmentation_preset)
-    layout += bool_layout(['Save segmentation visual'], preset= save_segmentation_visual_preset, keys=['save_segmentation_visual'])
-    layout += path_layout(keys=['saving path'], look_for_dir=True, preset=saving_path_preset)
-    layout += parameters_layout(['filename'], default_values=[filename_preset], size= 25)
+    object_col = sg.Column(layout)
 
-    return layout
+    #Reference dict
+    event_dict = {
+        key_2D : options_2D,
+        key_3D : options_3D,
+        object_key + "_radio_2D_seg" : radio_2D_seg,
+        object_key + "_radio_3D_seg" : radio_3D_seg,
+        object_key + "_channel" : channel_elmt, # For batch mode layout update
+    }
+
+    return object_col, event_dict
+    
 
 def _input_parameters_layout(
-        ask_for_segmentation,
-        is_3D_stack_preset,
-        time_stack_preset,
-        multichannel_preset,
-        do_dense_regions_deconvolution_preset,
-        do_clustering_preset,
-        do_segmentation_preset,
-        do_Napari_correction
-
-) :
+        ask_for_segmentation : bool,
+        is_3D_stack_preset : bool,
+        time_stack_preset : bool,
+        multichannel_preset : bool,
+        do_dense_regions_deconvolution_preset : bool,
+        do_clustering_preset : bool,
+        do_segmentation_preset : bool,
+        do_Napari_correction : bool
+    ) :
     layout_image_path = path_layout(['image_path'], header= "Image")
     layout_image_path += bool_layout(['3D stack', 'Multichannel stack'], keys=['is_3D_stack', 'is_multichannel'], preset= [is_3D_stack_preset, multichannel_preset])
     
     layout_image_path += bool_layout(
         ['Dense regions deconvolution', 'Compute clusters', 'Cell segmentation', 'Open Napari corrector'],
-        keys= ['do_dense_regions_deconvolution', 'do_cluster_computation', 'do_segmentation', 'show_napari_corrector'], 
+        keys= ['do_dense_regions_deconvolution', 'do_cluster_computation', 'do_segmentation','show_napari_corrector' ], 
         preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_segmentation_preset, do_Napari_correction], 
         header= "Pipeline settings")
 
@@ -298,21 +399,24 @@ def _detection_layout(
         do_segmentation,
         segmentation_done=False,
         default_dict : pipeline_parameters={},
-) :
+    ) :
     if is_3D_stack : dim = 3
     else : dim = 2
+    default = get_settings()
 
     #Detection
     detection_parameters = ['threshold', 'threshold penalty']
-    default_detection = [default_dict.setdefault('threshold',default.THRESHOLD), default_dict.setdefault('threshold penalty', default.THRESHOLD_PENALTY)]
+    default_detection = [default_dict.setdefault('threshold',default.threshold), default_dict.setdefault('threshold penalty', default.threshold_penalty)]
     opt= [True, True]
+    parameters_keys = ['threshold', 'threshold_penalty']
     if is_multichannel : 
-        detection_parameters += ['channel_to_compute']
+        detection_parameters += ['channel to compute']
         opt += [False]
-        default_detection += [default_dict.setdefault('channel_to_compute', '')]
+        parameters_keys += ['channel_to_compute']
+        default_detection += [default_dict.setdefault('channel_to_compute', default.detection_channel)]
     
     layout = [[sg.Text("Green parameters", text_color= 'green'), sg.Text(" are optional parameters.")]]
-    layout += parameters_layout(detection_parameters, header= 'Detection', opt=opt, default_values=default_detection)
+    layout += parameters_layout(detection_parameters, header= 'Detection', opt=opt, default_values=default_detection, keys= parameters_keys)
     
     if dim == 2 : tuple_shape = ('y','x')
     else : tuple_shape = ('z','y','x')
@@ -323,26 +427,26 @@ def _detection_layout(
     layout += tuple_layout(opt=opt, unit=unit, default_dict=default_dict, names=names, voxel_size= tuple_shape, spot_size= tuple_shape, log_kernel_size= tuple_shape, minimum_distance= tuple_shape)
     
     if (do_segmentation and is_multichannel) or (is_multichannel and segmentation_done):
-        layout += [[sg.Text("nucleus channel signal "), sg.InputText(default_text=default_dict.setdefault('nucleus_channel',default.NUC_CHANNEL), key= "nucleus channel signal", size= 5, tooltip= "Channel from which signal will be measured for nucleus features, \nallowing you to measure signal from a different channel than the one used for segmentation.")]]
+        layout += [[sg.Text("nucleus channel signal "), sg.InputText(default_text=default_dict.setdefault('nucleus_channel',default.nucleus_channel), key= "nucleus channel signal", size= 5, tooltip= "Channel from which signal will be measured for nucleus features, \nallowing you to measure signal from a different channel than the one used for segmentation.")]]
     
     #Deconvolution
     if do_dense_region_deconvolution :
-        default_dense_regions_deconvolution = [default_dict.setdefault('alpha',default.ALPHA), default_dict.setdefault('beta',default.BETA)]
+        default_dense_regions_deconvolution = [default_dict.setdefault('alpha',default.alpha), default_dict.setdefault('beta',default.beta)]
         layout += parameters_layout(['alpha', 'beta',], default_values= default_dense_regions_deconvolution, header= 'do_dense_regions_deconvolution')
-        layout += parameters_layout(['gamma'], unit= 'px', default_values= [default_dict.setdefault('gamma',default.GAMMA)])
+        layout += parameters_layout(['gamma'], unit= 'px', default_values= [default_dict.setdefault('gamma',default.gamma)])
         layout += tuple_layout(opt= {"deconvolution_kernel" : True}, unit= {"deconvolution_kernel" : 'px'}, default_dict=default_dict, deconvolution_kernel = tuple_shape)
     
     #Clustering
     if do_clustering :
-        layout += parameters_layout(['Cluster radius'],keys=['cluster_size'], unit="radius(nm)", default_values=[default_dict.setdefault('cluster_size',default.CLUSTER_SIZE)])
-        layout += parameters_layout(['Min nb spots per cluster'],keys=['min_number_of_spots'], default_values=[default_dict.setdefault('min_number_of_spots', default.MIN_NUMBER_SPOTS)])
+        layout += parameters_layout(['Cluster radius'],keys=['cluster_size'], unit="radius(nm)", default_values=[default_dict.setdefault('cluster_size',default.cluster_size)])
+        layout += parameters_layout(['Min nb spots per cluster'],keys=['min_number_of_spots'], default_values=[default_dict.setdefault('min_number_of_spots', default.min_spot)])
 
-    layout += bool_layout(['Interactive threshold selector'],keys = ['show_interactive_threshold_selector'], preset=[default.INTERACTIVE_THRESHOLD])
+    layout += bool_layout(['Interactive threshold selector'],keys = ['show_interactive_threshold_selector'], preset=[default.interactive_threshold_selector])
     layout += path_layout(
         keys=['spots_extraction_folder'],
         look_for_dir=True,
         header= "Individual spot extraction",
-        preset= default_dict.setdefault('spots_extraction_folder', default.SPOT_EXTRACTION_FOLDER)
+        preset= default_dict.setdefault('spots_extraction_folder', default.spot_extraction_folder)
     )
     default_filename = default_dict.setdefault("filename","") + "_spot_extraction"
     layout += parameters_layout(
@@ -353,39 +457,155 @@ def _detection_layout(
     layout += bool_layout(
         ['.csv','.excel',],
         keys= ['do_spots_csv', 'do_spots_excel'],
-        preset= [default_dict.setdefault('do_spots_csv',default.DO_CSV), default_dict.setdefault('do_spots_excel',default.DO_EXCEL),]
+        preset= [default_dict.setdefault('do_spots_csv',default.do_csv), default_dict.setdefault('do_spots_excel',default.do_excel),]
     )
 
     return layout
 
-def colocalization_layout(spot_list : list) :
-    layout = [
-        [sg.Push(), sg.Text("Co-localization", size=25, font="bold"), sg.Push()],
-        [sg.VPush()],
+def colocalization_layout(spot_list : list, **default_values) :
+    default = get_settings()
+
+    element_dict = {}
+    can_use_memory = len(spot_list) != 0
+
+    for spot_id in [1,2] :
+        element_dict[f"radio_spots{spot_id}_memory"] = sg.Radio("From memory : ", group_id = spot_id, enable_events = True, key = f"radio_spots{spot_id}_memory", default= can_use_memory or default_values.get(f"radio_spots{spot_id}_memory"), disabled= not can_use_memory)
+        element_dict[f"radio_spots{spot_id}_load"] = sg.Radio("Load spot detection : ", group_id = spot_id, enable_events = True, key = f"radio_spots{spot_id}_load", default= (not can_use_memory) or (default_values.get(f"radio_spots{spot_id}_load")))
+        
+        element_dict[f"spots{spot_id}_browse"] = [
+            sg.Input(size=20, key= f"spots{spot_id}_browse", default_text=default_values.get(f"spots{spot_id}_browse"), disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load")),
+            sg.FileBrowse(key=f"spots{spot_id}_browsebutton", initial_folder=default_values.setdefault(f"spots{spot_id}_browsebutton", default_values["working_directory"]), disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load")),
+        ]
+        element_dict[f"spots{spot_id}_voxel_size"] = [
+            sg.Text("voxel size"),
+            sg.Input(size= 5, key= f"z_voxel_size_spot{spot_id}", default_text= default_values.setdefault(f"z_voxel_size_spot{spot_id}", "z"), disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load")),
+            sg.Input(size= 5, key= f"y_voxel_size_spot{spot_id}", default_text= default_values.setdefault(f"y_voxel_size_spot{spot_id}", "y"), disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load")),
+            sg.Input(size= 5, key= f"x_voxel_size_spot{spot_id}", default_text= default_values.setdefault(f"x_voxel_size_spot{spot_id}", "x"), disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load")),
+        ]
+        
+        #Ref for updating
+        element_dict[f"options_spots{spot_id}_memory"] = sg.Col(
+            [[sg.DropDown(values=[""] + spot_list, key=f"spots{spot_id}_dropdown", size= 10, disabled= not can_use_memory or default_values.get(f"radio_spots{spot_id}_load"), default_value= default_values.setdefault(f"spots{spot_id}_dropdown", ""))]]
+            )
+        element_dict[f"options_spots{spot_id}_load"] = sg.Col(
+            [element_dict[f"spots{spot_id}_browse"], element_dict[f"spots{spot_id}_voxel_size"]]
+            )
+
+    col1 = sg.Col([
         [sg.Text("Spots 1", size = 10)],
-        [sg.DropDown(values=[""] + spot_list, key="spots1_dropdown"), sg.Input(disabled=True, text_color="black"),sg.FileBrowse("Load spot extraction", key="spots1_browse")],
+        [element_dict["radio_spots1_memory"]],
+        [element_dict["options_spots1_memory"]],
+        [element_dict["radio_spots1_load"]],
+        [element_dict["options_spots1_load"]],
+    ])
+
+    col2 = sg.Col([
         [sg.Text("Spots 2", size = 10)],
-        [sg.DropDown(values=[""] + spot_list, key="spots2_dropdown"), sg.Input(disabled=True, text_color="black"),sg.FileBrowse("Load spot extraction", key="spots2_browse")],
+        [element_dict["radio_spots2_memory"]],
+        [element_dict["options_spots2_memory"]],
+        [element_dict["radio_spots2_load"]],
+        [element_dict["options_spots2_load"]],
+    ])
+
+    layout = [
+        [sg.Push(), sg.Text("Co-localization", size=50, font="bold"), sg.Push()],
+        [sg.VPush()],
+        [col1,col2]
+    ]
+    layout += parameters_layout(['colocalisation distance'], unit= 'nm', default_values= [default_values.setdefault('colocalisation_distance', default_values["coloc_range"])])
+    layout += [[sg.Button("Ok", bind_return_key=True),sg.Button("Cancel"),sg.Push(),],
+        [sg.VPush()]
     ]
 
-    layout += parameters_layout(['colocalisation distance'], unit= 'nm', default_values= default.COLOC_RANGE,)
+    return layout, element_dict
 
-    layout += tuple_layout(opt={'voxel_size' : False},unit={'voxel_size' : "nm"}, voxel_size = ['z','y','x'], names={'voxel_size' : 'Voxel size'}, default_dict={'voxel_size' : default.COLOC_VOXEL_SIZE},)
-    layout += [[sg.Text("   'voxel size' is used only for loaded spot lists.")]]
+def settings_layout(default_values : SettingsDict = get_default_settings()) :
 
-    layout += [[sg.Push(),sg.Button("Ok", bind_return_key=True),sg.Button("Cancel"),sg.Push(),],
-        [sg.VPush()]
-    ]
+    if not isinstance(default_values, SettingsDict) : raise TypeError(f"Incorect type for default_values : {type(default_values)}; expected SettingsDict")
+    models_list = models.get_user_models() + models.MODEL_NAMES
+
+    layout = [[sg.Text("Default values", font="ArialBold 20")]]
+    layout += [[sg.Text("Default working directory"), sg.Input(default_text=default_values.working_directory, key= "working_directory"), sg.FolderBrowse()]]
+    
+    image_layout = [[sg.Text("Image", font="ArialBold 15")]]
+    image_layout += bool_layout(['Multichannel stack', '3D stack'],preset= [default_values.multichannel_stack, default_values.stack_3D], keys=["multichannel_stack", "stack_3D"])
+    image_layout += parameters_layout(['Detection channel', 'Nucleus channel'],default_values=[default_values.detection_channel, default_values.nucleus_channel], keys=['detection_channel', 'nucleus_channel'])
+
+    segmentation_layout = [[sg.Text("Segmentation", font="ArialBold 15")],
+                            [sg.Text("Cytoplasm model : "), sg.DropDown(models_list, default_value=default_values.cytoplasm_model, key= "cytoplasm_model")],
+                            [sg.Radio(default= default_values.cytoplasm_mean_proj, group_id=0, key="cytoplasm_mean_proj", text= "mean proj"), sg.Radio(default=default_values.cytoplasm_max_proj, group_id=0, key="cytoplasm_max_proj", text= "max proj"), sg.Radio(default= default_values.cytoplasm_select_slice, group_id=0, key="cytoplasm_select_slice", text= "single slice"), sg.Input(default_values.cytoplasm_selected_slice, size=5, key= "cytoplasm_selected_slice")],
+                            [sg.Text("Nucleus model : "), sg.DropDown(models_list, default_value=default_values.nucleus_model, key= "nucleus_model")],
+                            [sg.Radio(default= default_values.nucleus_mean_proj, group_id=1, key="nucleus_mean_proj", text= "mean proj"), sg.Radio(default= default_values.nucleus_max_proj, group_id=1, key="nucleus_max_proj", text= "max proj"), sg.Radio(default= default_values.nucleus_select_slice, group_id=1, key="nucleus_select_slice", text= "single slice"), sg.Input(default_values.nucleus_selected_slice, size=5, key= "nucleus_selected_slice")],
+                            ]
+    segmentation_layout += parameters_layout(
+        ["Flow threshold", "Cellprob threshold", "Cytoplasm diameter", "Cytoplasm min size", "Nucleus diameter", "Nucleus min size", "Anisotropy"],
+        default_values= [default_values.flow_threshold, default_values.cellprob_threshold, default_values.cytoplasm_diameter, default_values.cytoplasm_min_size, default_values.nucleus_diameter, default_values.nucleus_min_size, default_values.anisotropy], 
+        keys=["flow_threshold", "cellprob_threshold", "cytoplasm_diameter", "cytoplasm_min_size", "nucleus_diameter", "nucleus_min_size", "anisotropy"]) 
+    segmentation_layout += bool_layout(
+        ["show segmentation", "segment only nuclei", "do 3D segmentation", "save segmentation visual"], 
+        preset=[default_values.show_segmentation, default_values.segment_only_nuclei, default_values.do_3D_segmentation, default_values.save_segmentation_visuals],
+        keys= ["show_segmentation", "segment_only_nuclei", "do_3D_segmentation","save_segmentation_visuals"])
+
+    detection_layout = [[sg.Text("Detection", font="ArialBold 15")]]
+    detection_layout += parameters_layout(
+        ["Threshold", "Threshold penalty"],
+         default_values=[default_values.threshold, default_values.threshold_penalty],
+         keys=["threshold", "threshold_penalty"])
+    detection_layout += bool_layout(
+        ["Dense regions deconvolution", "Cluster computation", "show napari corrector", "Autofloresnce background removal", "interactive threshold selector"],
+        preset=[default_values.do_dense_regions_deconvolution, default_values.do_cluster, default_values.show_napari_corrector, default_values.do_background_removal, default_values.interactive_threshold_selector], 
+        keys=["do_dense_regions_deconvolution", "do_cluster", "show_napari_corrector","do_background_removal", "interactive_threshold_selector"])
+
+    deconvolution_layout = [[sg.Text("Dense regions deconvolution", font="ArialBold 15")]]
+    deconvolution_layout += parameters_layout(
+        ["alpha", "beta", "gamma"],
+        default_values=[default_values.alpha, default_values.beta, default_values.gamma]
+        )
+
+    clustering_layout = [[sg.Text("Cluster computation", font="ArialBold 15")]]
+    clustering_layout += parameters_layout(
+        ["Cluster size", "Min spot number"],
+        default_values=[default_values.cluster_size, default_values.min_spot], 
+        keys=["cluster_size", "min_spot"])
+
+    coloc_layout = [[sg.Text("Co-localization computation", font="ArialBold 15")]]
+    coloc_layout += parameters_layout(['Co-localization range'],
+    default_values=[default_values.coloc_range],
+     keys=['coloc_range'])
+    coloc_layout += tuple_layout(default_dict= {
+        'voxel_size_z' : default_values.voxel_size[0],
+        'voxel_size_y' : default_values.voxel_size[1],
+        'voxel_size_x' : default_values.voxel_size[2],
+        }, voxel_size=('z','y','x'))
+
+    spot_extraction_layout = [[sg.Text("Spots extraction", font="ArialBold 15")]]
+    spot_extraction_layout += bool_layout(
+        ["do csv", "do excel"],
+        preset=[default_values.do_csv, default_values.do_excel],
+        keys=["do_csv", "do_excel"]
+        )
+    spot_extraction_layout += [[sg.Text("spot extraction folder"), sg.Input(default_text=default_values.spot_extraction_folder, key="spot_extraction_folder", size=7) ,sg.FolderBrowse()]]
+
+    background_removing_layout = [[sg.Text("Background removing (batch)", font="ArialBold 15")]]
+    background_removing_layout += [
+        [sg.Checkbox("Remove background :", key= "do_background_removal", default= settings.do_background_removal)],
+        [sg.Text("Background channel : "), sg.Input(settings.background_channel, key = "background_channel", size= 5)]
+        ]
+
+    layout += [[sg.Col(image_layout, vertical_alignment='top', expand_x = True), sg.Col(background_removing_layout, vertical_alignment='top', expand_x = True)]]
+    layout += [[sg.Col(segmentation_layout, vertical_alignment='top', expand_x = True), sg.Col(detection_layout, vertical_alignment='top', expand_x = True)]]
+    layout += [[sg.Col(deconvolution_layout, vertical_alignment='top', expand_x = True), sg.Col(clustering_layout, vertical_alignment='top', expand_x = True)]]
+    layout += [[sg.Col(spot_extraction_layout, vertical_alignment='top', expand_x = True), sg.Col(coloc_layout, vertical_alignment='top', expand_x = True)]]
 
     return layout
 
 def _ask_channel_map_layout(
         shape,
         is_3D_stack,
-        multichannel,
+        is_multichannel,
         is_time_stack,
         preset_map={},
-) :
+    ) :
     
     x = preset_map.setdefault('x',0)
     y = preset_map.setdefault('y',0)
@@ -394,11 +614,11 @@ def _ask_channel_map_layout(
     t = preset_map.setdefault('t',0)
 
     layout = [
-            add_header("Dimensions mapping"), [sg.Text("Image shape : {0}".format(shape))]
+            [sg.Text("Dimensions mapping", font= "bold 15"), 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])
-    if multichannel : layout += parameters_layout(['c'], default_values=[c])
+    if is_multichannel : layout += parameters_layout(['c'], default_values=[c])
     if is_time_stack : layout += parameters_layout(['t'], default_values=[t])
 
     return layout