spacr 0.3.80__py3-none-any.whl → 0.3.81__py3-none-any.whl

spacr/gui_core.py

@@ -4,6 +4,7 @@ from tkinter import ttk
 from tkinter import filedialog
 from multiprocessing import Process, Value, Queue, set_start_method
 from tkinter import ttk
+import matplotlib
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 import numpy as np
@@ -324,17 +325,14 @@ def show_next_figure():
         index_control.set_to(len(figures) - 1)
         display_figure(fig)
 
-def process_fig_queue():
+def process_fig_queue_v1():
     global canvas, fig_queue, canvas_widget, parent_frame, uppdate_frequency, figures, figure_index, index_control
     from .gui_elements import standardize_figure
 
     #print("process_fig_queue called", flush=True)
     try:
-        got_new_figure = False
         while not fig_queue.empty():
             fig = fig_queue.get_nowait()
-            #print("Got a figure from fig_queue", flush=True)
-
             if fig is None:
                 print("Warning: Retrieved a None figure from fig_queue.", flush=True)
                 continue
@@ -345,30 +343,63 @@ def process_fig_queue():
 
             # Update slider maximum
             index_control.set_to(len(figures) - 1)
-            #print("New maximum slider value after adding a figure:", index_control.to, flush=True)
 
             # If no figure has been displayed yet
             if figure_index == -1:
                 figure_index = 0
                 display_figure(figures[figure_index])
                 index_control.set(figure_index)
-                #print("Displayed the first figure and set slider value to 0", flush=True)
 
-            #got_new_figure = True
+    except Exception as e:
+        print("Exception in process_fig_queue:", e, flush=True)
+        traceback.print_exc()
 
-        #if not got_new_figure:
-            # No new figures this time
-            #print("No new figures found in the queue this iteration.", flush=True)
+    finally:
+        # Schedule process_fig_queue() to run again
+        after_id = canvas_widget.after(uppdate_frequency, process_fig_queue)
+        parent_frame.after_tasks.append(after_id)
+        
+def process_fig_queue():
+    global canvas, fig_queue, canvas_widget, parent_frame, uppdate_frequency, figures, figure_index, index_control
+    from .gui_elements import standardize_figure
+
+    try:
+        while not fig_queue.empty():
+            fig = fig_queue.get_nowait()
+            if fig is None:
+                print("Warning: Retrieved a None figure from fig_queue.")
+                continue
+
+            # Standardize the figure appearance before adding it
+            fig = standardize_figure(fig)
+            figures.append(fig)
+
+            # OPTIONAL: Cap the size of the figures deque at 100
+            MAX_FIGURES = 100
+            while len(figures) > MAX_FIGURES:
+                # Discard the oldest figure
+                old_fig = figures.popleft()
+                # If needed, you could also close the figure to free memory:
+                matplotlib.pyplot.close(old_fig)
+
+            # Update slider maximum
+            index_control.set_to(len(figures) - 1)
+
+            # If no figure has been displayed yet
+            if figure_index == -1:
+                figure_index = 0
+                display_figure(figures[figure_index])
+                index_control.set(figure_index)
 
     except Exception as e:
-        print("Exception in process_fig_queue:", e, flush=True)
+        print("Exception in process_fig_queue:", e)
         traceback.print_exc()
 
     finally:
         # Schedule process_fig_queue() to run again
         after_id = canvas_widget.after(uppdate_frequency, process_fig_queue)
         parent_frame.after_tasks.append(after_id)
-        #print("process_fig_queue scheduled again", flush=True)
+
 
 def update_figure(value):
     from .gui_elements import standardize_figure

spacr/gui_elements.py

@@ -17,8 +17,7 @@ from skimage.draw import polygon, line
 from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
 from tkinter import ttk, scrolledtext
-from skimage.color import rgb2gray 
-
+from skimage.color import rgb2gray
 fig = None
 
 def create_menu_bar(root):

spacr/settings.py

@@ -885,9 +885,32 @@ expected_types = {
     "cmap":str,
     "pathogen_model":str,
     "normalize_input":bool,
+    "filter_column":str,
+    "target_unique_count":int,
+    "threshold_multiplier":int,
+    "threshold_method":str,
+    "count_data":list,
+    "score_data":list,
+    "min_n":int,
+    "controls":list,
+    "toxo":bool,
+    "volcano":str,
+    "metadata_files":list,
+    "filter_value":list,
+    "split_axis_lims":str,
+    "x_lim":(list,None),
+    "log_x":bool,
+    "log_y":bool,
+    "reg_alpha":(int,float),
+    "reg_lambda":(int,float),
+    "prune_features":bool,
+    "cross_validation":bool,
+    "offset_start":int,
+    "chunk_size":int,
+    "single_direction":str,
 }
 
-categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset","model_path","grna_csv","row_csv","column_csv"],
+categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset","model_path","grna_csv","row_csv","column_csv", "metadata_files", "score_data","count_data"],
              "General": ["metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model", "segmentation_mode"],
              "Cellpose":["fill_in","from_scratch", "n_epochs", "width_height", "model_name", "custom_model", "resample", "rescale", "CP_prob", "flow_threshold", "percentiles", "invert", "diameter", "grayscale", "Signal_to_noise", "resize", "target_height", "target_width"],
              "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "uninfected", "merge_edge_pathogen_cells", "adjust_cells", "cells", "cell_loc"],
@@ -895,18 +918,18 @@ categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset
              "Pathogen": ["pathogen_intensity_range", "pathogen_size_range", "pathogen_chann_dim", "pathogen_channel", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogen_mask_dim", "pathogens", "pathogen_loc", "pathogen_types", "pathogen_plate_metadata", ],
              "Measurements": ["remove_image_canvas", "remove_highly_correlated", "homogeneity", "homogeneity_distances", "radial_dist", "calculate_correlation", "manders_thresholds", "save_measurements", "tables", "image_nr", "dot_size", "filter_by", "remove_highly_correlated_features", "remove_low_variance_features", "channel_of_interest"],
              "Object Image": ["save_png", "dialate_pngs", "dialate_png_ratios", "png_size", "png_dims", "save_arrays", "normalize_by", "crop_mode", "normalize", "use_bounding_box"],
-             "Sequencing": ["signal_direction","mode","comp_level","comp_type","save_h5","expected_end","offset","target_sequence","regex", "highlight"],
+             "Sequencing": ["offset_start","chunk_size","single_direction", "signal_direction","mode","comp_level","comp_type","save_h5","expected_end","offset","target_sequence","regex", "highlight"],
              "Generate Dataset":["save_to_db","file_metadata","class_metadata", "annotation_column","annotated_classes", "dataset_mode", "metadata_type_by","custom_measurement", "sample", "size"],
              "Hyperparamiters (Training)": ["png_type", "score_threshold","file_type", "train_channels", "epochs", "loss_type", "optimizer_type","image_size","val_split","learning_rate","weight_decay","dropout_rate", "init_weights", "train", "classes", "augment", "amsgrad","use_checkpoint","gradient_accumulation","gradient_accumulation_steps","intermedeate_save","pin_memory"],
              "Hyperparamiters (Embedding)": ["visualize","n_neighbors","min_dist","metric","resnet_features","reduction_method","embedding_by_controls","col_to_compare","log_data"],
              "Hyperparamiters (Clustering)": ["eps","min_samples","analyze_clusters","clustering","remove_cluster_noise"],
-             "Hyperparamiters (Regression)":["cov_type", "class_1_threshold", "plate", "other", "fraction_threshold", "alpha", "random_row_column_effects", "regression_type", "min_cell_count", "agg_type", "transform", "dependent_variable"],
+             "Hyperparamiters (Regression)":["cross_validation","prune_features","reg_lambda","reg_alpha","cov_type", "class_1_threshold", "plate", "other", "fraction_threshold", "alpha", "random_row_column_effects", "regression_type", "min_cell_count", "agg_type", "transform", "dependent_variable"],
              "Hyperparamiters (Activation)":["cam_type", "overlay", "correlation", "target_layer", "normalize_input"],
-             "Annotation": ["nc_loc", "pc_loc", "nc", "pc", "cell_plate_metadata","treatment_plate_metadata", "metadata_types", "cell_types", "target","positive_control","negative_control", "location_column", "treatment_loc", "channel_of_interest", "measurement", "treatments", "um_per_pixel", "nr_imgs", "exclude", "exclude_conditions", "mix", "pos", "neg"],
-             "Plot": ["plot", "plot_control", "plot_nr", "examples_to_plot", "normalize_plots", "cmap", "figuresize", "plot_cluster_grids", "img_zoom", "row_limit", "color_by", "plot_images", "smooth_lines", "plot_points", "plot_outlines", "black_background", "plot_by_cluster", "heatmap_feature","grouping","min_max","cmap","save_figure"],
+             "Annotation": ["filter_column", "filter_value","volcano", "toxo", "controls", "nc_loc", "pc_loc", "nc", "pc", "cell_plate_metadata","treatment_plate_metadata", "metadata_types", "cell_types", "target","positive_control","negative_control", "location_column", "treatment_loc", "channel_of_interest", "measurement", "treatments", "um_per_pixel", "nr_imgs", "exclude", "exclude_conditions", "mix", "pos", "neg"],
+             "Plot": ["plot", "split_axis_lims", "x_lim","log_x","log_y", "plot_control", "plot_nr", "examples_to_plot", "normalize_plots", "cmap", "figuresize", "plot_cluster_grids", "img_zoom", "row_limit", "color_by", "plot_images", "smooth_lines", "plot_points", "plot_outlines", "black_background", "plot_by_cluster", "heatmap_feature","grouping","min_max","cmap","save_figure"],
              "Test": ["test_mode", "test_images", "random_test", "test_nr", "test", "test_split"],
              "Timelapse": ["timelapse", "fps", "timelapse_displacement", "timelapse_memory", "timelapse_frame_limits", "timelapse_remove_transient", "timelapse_mode", "timelapse_objects", "compartments"],
-             "Advanced": ["shuffle", "target_intensity_min", "cells_per_well", "nuclei_limit", "pathogen_limit", "background", "backgrounds", "schedule", "test_size","exclude","n_repeats","top_features", "model_type_ml", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs"],
+             "Advanced": ["target_unique_count","threshold_multiplier", "threshold_method", "min_n","shuffle", "target_intensity_min", "cells_per_well", "nuclei_limit", "pathogen_limit", "background", "backgrounds", "schedule", "test_size","exclude","n_repeats","top_features", "model_type_ml", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs"],
              "Miscellaneous": ["all_to_mip", "pick_slice", "skip_mode", "upscale", "upscale_factor"]
              }
 

spacr/utils.py

@@ -5045,19 +5045,22 @@ def generate_cytoplasm_mask(nucleus_mask, cell_mask):
     return cytoplasm_mask
 
 def add_column_to_database(settings):
-    """
-    Adds a new column to the database table by matching on a common column from the DataFrame.
-    If the column already exists in the database, it adds the column with a suffix.
-    NaN values will remain as NULL in the database.
-    
-    Parameters:
-    - settings: A dictionary containing the following keys:
-        - 'csv_path': Path to the CSV file with the data to be added.
-        - 'db_path': Path to the SQLite database (or connection string for other databases).
-        - 'table_name': The name of the table in the database.
-        - 'update_column': The name of the new column in the DataFrame to add to the database.
-        - 'match_column': The common column used to match rows.
-    """
+    #"""
+    #Adds a new column to the database table by matching on a common column from the DataFrame.
+    #If the column already exists in the database, it adds the column with a suffix.
+    #NaN values will remain as NULL in the database.
+
+    #Parameters:
+    #    settings (dict): A dictionary containing the following keys:
+    #    csv_path (str): Path to the CSV file with the data to be added.
+    #    db_path (str): Path to the SQLite database (or connection string for other databases).
+    #    table_name (str): The name of the table in the database.
+    #    update_column (str): The name of the new column in the DataFrame to add to the database.
+    #    match_column (str): The common column used to match rows.
+
+    #Returns:
+    #    None
+    #"""
 
     # Read the DataFrame from the provided CSV path
     df = pd.read_csv(settings['csv_path'])

{spacr-0.3.80.dist-info → spacr-0.3.81.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.80
+Version: 0.3.81
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.80.dist-info → spacr-0.3.81.dist-info}/RECORD

@@ -12,8 +12,8 @@ spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
 spacr/core.py,sha256=3u2qKmPmTlswvE1uKTF4gi7KQ3sJBHV9No_ysgk7JCU,48487
 spacr/deep_spacr.py,sha256=V3diLyxX-0_F5UxhX_b94ROOvL9eoLvnoUmF3nMBqPQ,43250
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
-spacr/gui_core.py,sha256=6NKv8ebqC9Zuior4f2-L1By_Pjtt-RPCrEgnRuE9P54,45576
-spacr/gui_elements.py,sha256=I_eSYF1RkAG0zsa-ZiQT0EaaVvUpucULCuWCowO6t4E,138248
+spacr/gui_core.py,sha256=3S1S7rOtGfm5Z-Fb-jk1HxjsLZo6IboBxtXtsDMw1ME,46578
+spacr/gui_elements.py,sha256=fc9z-GP_PmtJy2lIsfi3fx5r5puTJ-zz8ntB9pC53Gc,138246
 spacr/gui_utils.py,sha256=u9RoIOWpAXFEOnUlLpMQZrc1pWSg6omZsJMIhJdRv_g,41211
 spacr/io.py,sha256=LF6lpphw7GSeuoHQijPykjKNF56wNTFEWFZuDQp3O6Q,145739
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
@@ -23,13 +23,13 @@ spacr/ml.py,sha256=x19S8OsR5omb8e6MU9I99Nz95J_QvM5siyk-zaAU3p8,82866
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
 spacr/plot.py,sha256=gXC7y3uT4sx8KRODeSFWQG_A1CylsuJ5B7HYe_un6so,165177
 spacr/sequencing.py,sha256=ClUfwPPK6rNUbUuiEkzcwakzVyDKKUMv9ricrxT8qQY,25227
-spacr/settings.py,sha256=xTFTD04H8uXRJ5m4Pnr4Znhx0f_FxdgStMPXol3apxM,80888
+spacr/settings.py,sha256=3bgBWBotIO7TZx2nh6JoEaqHNmwbChAiz1gW4xmURQs,81788
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
 spacr/submodules.py,sha256=SK8YEs850LAx30YAiwap7ecLpp1_p-bci6H-Or0GLoA,55500
 spacr/timelapse.py,sha256=KGfG4L4-QnFfgbF7L6C5wL_3gd_rqr05Foje6RsoTBg,39603
 spacr/toxo.py,sha256=z2nT5aAze3NUIlwnBQcnkARihDwoPfqOgQIVoUluyK0,25087
-spacr/utils.py,sha256=SiUcctyUETEX_GZ-Nflba5whZiEjJynncaH-xcZPK1k,222242
+spacr/utils.py,sha256=jjZIqzJKl9nnWgj2eJiLFT27gED8hO6rAEsJLlimm-E,222298
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -152,9 +152,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.80.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.80.dist-info/METADATA,sha256=Q0YV4N-C8XyUHH8HFW_k9ryAftcU8v9oMxNhgzvU8cA,6032
-spacr-0.3.80.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.80.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.80.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.80.dist-info/RECORD,,
+spacr-0.3.81.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.81.dist-info/METADATA,sha256=TneYaiWWfNHUuqpSQpRAEzWzYia6KIksYDzNVDcsimw,6032
+spacr-0.3.81.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.81.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.81.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.81.dist-info/RECORD,,