Merge branch 'intensity-masking' of https://github.com/computational-cell-analytics/lightsheet-moser into intensity-masking

Author: constantinpape

scripts/la-vision/otof/import_cochlea.py

@@ -0,0 +1,46 @@
+import os
+import h5py
+from mobie import add_image
+from mobie.metadata import read_dataset_metadata
+
+INPUT_PATH = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/LA_VISION_OTOF/Test_FreeRotate_0-40-59_PRO82_OtofKO-23R_p24_chCR-488_rbOtof-647_UltraII_C00_xyz.ims"  # noqa
+MOBIE_ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/mobie_project/cochlea-lightsheet"
+DS_NAME = "LaVision-OTOF"
+RESOLUTION = (3.0, 1.887779, 1.887779)
+
+
+# Channels: "chCR-488_rbOtof-647"
+def add_otof():
+    channel_names = ("CR", "rbOtof")
+    channel_keys = [
+        "/DataSet/ResolutionLevel 0/TimePoint 0/Channel 0/Data",
+        "/DataSet/ResolutionLevel 0/TimePoint 0/Channel 1/Data"
+    ]
+
+    scale_factors = 4 * [[2, 2, 2]]
+    chunks = (96, 96, 96)
+
+    for channel_key, channel_name in zip(channel_keys, channel_names):
+        mobie_ds_folder = os.path.join(MOBIE_ROOT, DS_NAME)
+        ds_metadata = read_dataset_metadata(mobie_ds_folder)
+        if channel_name in ds_metadata.get("sources", {}):
+            print(channel_name, "is already in MoBIE")
+            continue
+
+        print("Load image data ...")
+        with h5py.File(INPUT_PATH, "r") as f:
+            input_data = f[channel_key][:]
+        print(input_data.shape)
+        add_image(
+            input_path=input_data, input_key=None, root=MOBIE_ROOT,
+            dataset_name=DS_NAME, image_name=channel_name, resolution=RESOLUTION,
+            scale_factors=scale_factors, chunks=chunks, unit="micrometer", use_memmap=False,
+        )
+
+
+def main():
+    add_otof()
+
+
+if __name__ == "__main__":
+    main()

scripts/la-vision/otof/upload_otof_lsm.sh

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+#!/bin/bash
+
+MOBIE_DIR=/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/mobie_project/cochlea-lightsheet
+COCHLEA=LaVision-OTOF
+
+export BUCKET_NAME="cochlea-lightsheet"
+export SERVICE_ENDPOINT="https://s3.fs.gwdg.de"
+mobie.add_remote_metadata -i $MOBIE_DIR -s $SERVICE_ENDPOINT -b $BUCKET_NAME
+
+# rclone --progress copyto "$MOBIE_DIR"/"$COCHLEA" cochlea-lightsheet:cochlea-lightsheet/"$COCHLEA"
+# rclone --progress copyto "$MOBIE_DIR"/project.json cochlea-lightsheet:cochlea-lightsheet/project.json