small-fish-gui 1.9.4__py3-none-any.whl → 1.10.1__py3-none-any.whl

small_fish_gui/gui/help_module.py

@@ -1,256 +0,0 @@
-import FreeSimpleGUI as sg
-import os
-
-
-def _fake_help() :
-    layout = [
-        [sg.Text("Fake help window")],
-        [sg.Button('Close')]
-    ]
-
-    return layout
-
-def ask_help(chapter= '') :
-    
-    if chapter == 'general' :
-        help_l = _general_help()
-
-    elif chapter == 'segmentation' :
-        help_l= _segmentation_help()
-
-    elif chapter == 'mapping' : 
-        help_l = _mapping_help()
-
-    elif chapter == 'detection' :
-        help_l = _detection_help()
-
-    else : 
-        help_l = _fake_help()
-
-    window = sg.Window('Help (small fish)', layout=help_l, keep_on_top=True, auto_size_text=True)
-    event, values = window.read(timeout= 0.1)
-
-    if event == 'Close' :
-        window.close()
-
-def add_help_button(help_request) :
-    pass
-
-def _general_help() :
-
-    im_path = os.path.dirname(__file__) + '/general_help_screenshot.png'
-
-    help_text = """
-    Pipeline settings :
-
-        do_dense_regions_deconvolution : (Recommanded for cluster computations) Detect dense and bright regions with potential clustered 
-            spots and simulate a more realistic number of spots in these regions.
-            See bigfish documentation : https://big-fish.readthedocs.io/en/stable/detection/dense.html
-
-        do_cluster_computation :
-            DBScan algorithm is ran by big-fish to detecte clusters of spots. Use is you want to quantify one of the following : 
-            Transcription sites, foci, colocalisation of spots near foci...
-        
-        Segmentation : Perform full cell segmentation in 2D (cytoplasm + nucleus) via cellpose.
-            You can use your own retrained models or out of the box models from cellpose.
-
-        Napari correct :
-            After each detection, opens a Napari viewer, enabling the user to visualise, add or remove spots and clusters.
-    """
-
-    layout = [
-        [sg.Text("Welcome to small fish", font= 'bold 15')],
-        [sg.Image(im_path)],
-        [sg.Text(help_text, font = 'bold 10')]
-    ]
-
-    return layout
-
-def _detection_help() :
-
-    header = """
-    Detection is the main feature we use from big-fish package (usage requires quote).
-    Access fully detailed documentation : 
-    
-        DETECTION : https://big-fish.readthedocs.io/en/stable/detection/spots.html
-        do_dense_regions_deconvolution : https://big-fish.readthedocs.io/en/stable/detection/dense.html
-        CLUSTERING : https://big-fish.readthedocs.io/en/stable/detection/cluster.html
-        
-    """
-    detection_header= """
-    
-    DETECTION PARAMETERS
-    """
-    detection_text = """
-    threshold
-        Leave empty for automatic threshold computation (see doc). Or set a manual threshold to apply after LoG filter.
-    
-    threshold penalty
-        Custom feature. Apply a multiplicator to automatic threshold.
-        Leave empty or 1 for no modification of auto threshold.
-        From 0<.<1 values will lower the threshold, increasing the number of spot detected.
-        On the contrary >1 values will increase the threshold, reducing the number of spot detected.
-             
-    voxel_size
-        Size of a voxel, in nanometer. One value per spatial dimension (zyx or yx dimensions). 
-        If it’s a scalar, the same value is applied to every dimensions. Not used if ‘log_kernel_size’ and ‘minimum_distance’ are provided.
-
-    spot_size    
-        Radius of the spot, in nanometer. One value per spatial dimension (zyx or yx dimensions). 
-        If it’s a scalar, the same radius is applied to every dimensions. 
-        Not used if ‘log_kernel_size’ and ‘minimum_distance’ are provided.
-
-    log kernel size
-        Size of the LoG kernel. It equals the standard deviation (in pixels) used for the gaussian kernel 
-        (one for each dimension). One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, 
-        the same standard deviation is applied to every dimensions. 
-        If None, we estimate it with the voxel size and spot radius.
-
-    minimum distance
-        Minimum distance (in pixels) between two spots we want to be able to detect separately. 
-        One value per spatial dimension (zyx or yx dimensions). 
-        If it’s a scalar, the same distance is applied to every dimensions. 
-        If None, we estimate it with the voxel size and spot radius.
-
-    """
-    deconv_header="""    
-    do_dense_regions_deconvolution PARAMETERS
-
-    """
-    deconv_text="""
-    alpha
-        Note : Simply put the higher alpha the less spots are added in bright regions.
-
-        Intensity percentile used to compute the reference spot, between 0 and 1. 
-        The higher, the brighter are the spots simulated in the dense regions. 
-        Consequently, a high intensity score reduces the number of spots added. 
-        Default is 0.5, meaning the reference spot considered is the median spot.
-    
-    beta
-        Note : Simply put the higher beta the brighter regions need to be to be deconvoluted.
-
-        Multiplicative factor for the intensity threshold of a dense region. Default is 1. 
-        Threshold is computed with the formula:
-
-                threshold = beta * max(median_spot)
-
-        with median_spot the median value of all detected spot signals.
-    
-    gamma
-        Note : for gamma = 0 no gaussian filter is performed.
-
-        Multiplicative factor use to compute the gaussian kernel size:
-
-                kernel_size = gamma * spot_size / voxel_size
-
-        We perform a large gaussian filter with such scale to estimate image background and remove it from original image. 
-        A large gamma increases the scale of the gaussian filter and smooth the estimated background. 
-        To decompose very large bright areas, a larger gamma should be set.
-
-    kernel_size
-        Standard deviation used for the gaussian kernel (one for each dimension), in pixel. 
-        If it’s a scalar, the same standard deviation is applied to every dimensions. 
-        If None, we estimate the kernel size from ‘spot_radius’, ‘voxel_size’ and ‘gamma’
-
-
-    """
-    clustering_header="""    
-    CLUSTERING PARAMETERS
-
-    """
-    clustering_text="""
-    cluster size
-        The maximum distance between two samples for one to be considered as in the neighborhood of the other. 
-        Radius expressed in nanometer.
-        
-        NOTE : Cluster centroids are computed from bigfish DBScan algorithm. 
-        But the number of spots belonging to those clusters is computed as the number of sptos closer than the cluster_size distance (nanometer).
-        Which can yield a slightly different result than bigfish but allow us to add and delete cluster with the napari correction option.
-
-    min number of spots
-        The number of spots in a neighborhood for a point to be considered as a core point (from which a cluster is expanded). 
-        This includes the point itself.
-
-    """
-
-    quote = """
-    BigFish quote : 
-    Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. 
-    FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) 
-    https://doi.org/10.1101/2021.07.20.45302
-
-    """
-
-    layout = [
-        [sg.Text(header, font= "bold 15")],
-        [sg.Column([
-            [sg.Text(detection_header, font= 'bold 13')],
-            [sg.Text(detection_text)],
-            [sg.Text(deconv_header, font= 'bold 13')],
-            [sg.Text(deconv_text)],
-            [sg.Text(clustering_header, font= 'bold 13')],
-            [sg.Text(clustering_text)],
-            ], scrollable=True, vertical_scroll_only=True)],
-        [sg.Text(quote, font= 'italic 8')]
-    ]
-
-    return layout
-
-def _segmentation_help() :
-
-    cellpose1_quote = """Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021).
-    Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106."""
-    cellpose2_quote = """Pachitariu, M. & Stringer, C. (2022).
-    Cellpose 2.0: how to train your own model. Nature methods, 1-8."""
-    im_path = os.path.dirname(__file__) + '/segmentation_help_screenshot.png'
-
-    layout =[
-        [sg.Text("Segmentation is performed using Cellpose 2.0; this is published work that requires citation.\n")],
-        [sg.Text(cellpose1_quote)],
-        [sg.Text(cellpose2_quote)],
-        [sg.Image(im_path)]
-    ]
-
-    return layout
-
-
-def _mapping_help() :
-
-    im_path = os.path.dirname(__file__) + '/mapping_help_screenshot.png'
-
-
-    help_text = """
-    Depending on image format, dimensions (time, channels, spatial dimensions) are not always stored in the same order.
-    An automatic configuration is performed; nonetheless it is recommanded to check it worked properly or your data can
-    get mixed up.
-
-    This window present the shape of your image : example (1080,1080,4)
-    1080x1080 are the xy dimension (pixel resolution); and 4 is the number of channel. Another example a 3D multichannel 
-    stack could be (18,4,1080,1080)...
-    The machine understand the order of the information such as (1080,1080,4) positions are (0,1,2). It starts from zero!
-    The mapping purpose is to link the position to the type of informations, in this case we want :
-
-            x : 1
-            y : 0
-            z : None
-            c : 2
-            t : None
-
-    The other example from above (18,4,1080,1080) mapping would be :
-
-            x : 3
-            y : 2
-            z : 0
-            c : 1
-            t : None
-    """
-
-    layout = [
-        [sg.Text(help_text)],
-        [sg.Image(im_path)]
-    ]
-
-    return layout
-
-def _small_fish_help() :
-    pass

small_fish_gui-1.9.4.dist-info/RECORD

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