Merge pull request #40 from TeamNCMC/duplicate-examples

Duplicate examples

Author: guillaumelegoc

cuisto/config.py

@@ -4,6 +4,7 @@
 
 """
 
+import os
 import tomllib
 import warnings
 
@@ -62,9 +63,10 @@ def __init__(self, config_file):
     def get_blacklist(self):
         """Wraps cuisto.utils.get_blacklist."""
 
-        self.atlas["blacklist"] = utils.get_blacklist(
-            self.files["blacklist"], self.bg_atlas
-        )
+        if os.path.isfile(self.files["blacklist"]):
+            self.atlas["blacklist"] = utils.get_blacklist(
+                self.files["blacklist"], self.bg_atlas
+            )
 
     def get_leaves_list(self):
         """Wraps utils.get_leaves_list."""

examples/cells_distributions.py

@@ -24,24 +24,30 @@
 
 from pathlib import Path
 
+import matplotlib.pyplot as plt
 import pandas as pd
 
 import cuisto
 
 # Full path to your configuration file, edited according to your need beforehand
-wdir = Path(__file__).parent.parent
-config_file = wdir / "resources" / "demo_config_cells.toml"
+wdir = Path(__file__).parent.parent / "resources"
+config_file = wdir / "demo_config_cells.toml"
 
 # - Files
 # animal identifier
 animal = "animalid0"
 # set the full path to the annotations tsv file from QuPath
-annotations_file = "../../resources/cells_measurements_annotations.tsv"
+annotations_file = wdir / "cells_measurements_annotations.tsv"
 # set the full path to the detections tsv file from QuPath
-detections_file = "../../resources/cells_measurements_detections.tsv"
+detections_file = wdir / "cells_measurements_detections.tsv"
 
 # get configuration
 cfg = cuisto.config.Config(config_file)
+# update configuration file paths (so that this example can self-run)
+cfg.files["blacklist"] = wdir / "demo_atlas_blacklist_brain.toml"
+cfg.files["fusion"] = wdir / "demo_atlas_fusion_brain.toml"
+cfg.files["infos"] = wdir / "demo_info_cells.toml"
+cfg.get_blacklist()
 
 # read data
 df_annotations = pd.read_csv(annotations_file, index_col="Object ID", sep="\t")
@@ -87,3 +93,5 @@
 
 # plot heatmap (all types of cells pooled)
 fig_heatmap = cuisto.display.plot_2D_distributions(df_coordinates, cfg)
+
+plt.show()

examples/density_map.py

@@ -15,14 +15,17 @@
 # Find this script as a notebook in the documentation :
 # https://teamncmc.github.io/cuisto/demo_notebooks/density_map.html
 
+from pathlib import Path
+
 import brainglobe_heatmap as bgh
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import seaborn as sns
 
 # path to the exported measurements from QuPath
-filename = "../resources/cells_measurements_detections.tsv"
+wdir = Path(__file__).parent.parent / "resources"
+filename = wdir / "cells_measurements_detections.tsv"
 
 # Settings
 # atlas to use
@@ -160,3 +163,5 @@
 plt.yticks([])
 plt.plot([0.5, 1.5], [0.5, 0.5], "k", linewidth=3)
 plt.text(0.5, 0.4, "1 mm")
+
+plt.show()