Source code to visualize SMLM data via Napari

scripts/smlm_napari.py

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+import napari
+import pathlib
+import numpy as np
+from vispy.color import Colormap
+from shareloc_utils.smlm_file import read_smlm_file, plot_histogram
+from shareloc_utils.batch_download import download
+
+def plot_smlm_in_napari(output_dir,
+                        datasets = 5514120, #Znodo DOI number
+                        extension = ".smlm"):
+    datasets=str(datasets)
+    list_path=list(pathlib.Path(output_dir+datasets).glob('*/*/*.smlm'))
+    # down load
+    if not list_path:
+        download(
+        datasets=[datasets],
+        output_dir=output_dir+datasets,
+        extension=extension,
+        conversion=False,
+        sandbox=False)
+
+    redhot_cmap=Colormap([[0, 0, 0], [1, 0, 0],[1, 1, 0], [1, 1, 1]])
+    cmap = [redhot_cmap, 'cyan', 'green', 'magenta']
+
+    for sample_index in range(len(list_path)):
+        viewer = napari.Viewer()
+        print("plotting: ",list_path[sample_index])
+        imag_path = list_path[sample_index]
+        manifest = read_smlm_file(imag_path)
+        tables = manifest["files"]
+        histogram = []
+        name = []
+        colormap = []
+        for ch in range(len(tables)):
+        #histogram.append(plot_histogram(tables[ch]["data"], value_range=(0, 255)))
+        #print(np.shape(histogram))
+        #histogram = np.concatenate((histogram, plot_histogram(tables[ch]["data"], value_range=(0, 255))[:,:,np.newaxis]), axis=-1)
+            histogram = plot_histogram(tables[ch]["data"], value_range=(0, 255))
+            name.append(tables[ch]["name"])
+            colormap.append(cmap[ch])
+            viewer.add_image(
+                histogram,
+                blending="additive",
+                colormap=cmap[ch],
+                contrast_limits=[0, 10],
+                name=tables[ch]["name"])
+
+def main():
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Visualize locally SMLM data via napari")
+    parser.add_argument(
+        "--datasets",
+        default=[],
+        help="A Zenodo ID XXXX",
+    )
+    parser.add_argument("--output_dir", default=None, help="output directory path")
+    parser.add_argument(
+        "--sandbox",
+        action="store_true",
+        help="Use the sandbox site, used only when Zenodo IDs are provided for the datasets",
+    )
+    parser.add_argument(
+        "--conversion",
+        action="store_true",
+        help="enable conversion to text file (e.g. csv)",
+    )
+    parser.add_argument(
+        "--extension", default=".smlm", help="file extension for text file conversion"
+    )
+
+    args = parser.parse_args()
+
+    plot_smlm_in_napari(output_dir = args.output_dir,
+                        datasets = args.datasets, #Znodo DOI number
+                        extension = args.extension)
+    napari.run()
+
+
+if __name__ == "__main__":
+    main()