Merge branch 'master' of https://github.com/computational-cell-analytics/flamingo-tools

Author: constantinpape

flamingo_tools/data_conversion.py

@@ -207,9 +207,42 @@ def _write_missing_views(out_path):
     tree.write(xml_path)
 
 
+def _parse_shape(metadata_file):
+    depth, height, width = None, None, None
+
+    with open(metadata_file, "r") as f:
+        for line in f.readlines():
+            line = line.strip().rstrip("\n")
+            if line.startswith("AOI width"):
+                width = int(line.split(" ")[-1])
+            if line.startswith("AOI height"):
+                height = int(line.split(" ")[-1])
+            if line.startswith("Number of planes saved"):
+                depth = int(line.split(" ")[-1])
+
+    assert depth is not None
+    assert height is not None
+    assert width is not None
+    return (depth, height, width)
+
+
+def _load_data(file_path, metadata_file):
+    if Path(file_path).suffix == ".raw":
+        shape = _parse_shape(metadata_file)
+        data = np.memmap(file_path, mode="r", dtype="uint16", shape=shape)
+    else:
+        try:
+            data = tifffile.memmap(file_path, mode="r")
+        except ValueError:
+            print(f"Could not memmap the data from {file_path}. Fall back to load it into memory.")
+            data = tifffile.imread(file_path)
+    return data
+
+
 def convert_lightsheet_to_bdv(
     root: str,
     out_path: str,
+    file_ext: str = ".tif",
     attribute_parser: callable = flamingo_filename_parser,
     attribute_names: Optional[Dict[str, Dict[int, str]]] = None,
     metadata_file_name_pattern: Optional[str] = None,
@@ -233,6 +266,8 @@ def convert_lightsheet_to_bdv(
         root: Folder that contains the image data stored as tifs.
             This function will take into account all tif files in folders beneath this root directory.
         out_path: Output path where the converted data is saved.
+        file_ext: The name of the file extension. By default assumes tif files (.tif).
+            Change to '.raw' to read files stored in raw format instead.
         attribute_parser: TODO
         metadata_file_name_pattern: The pattern for the names of files that contain the metadata.
             For flamingo metadata the following pattern should work: '*_Settings.txt'.
@@ -264,7 +299,11 @@ def convert_lightsheet_to_bdv(
     elif ext == ".zarr":
         convert_to_ome_zarr = True
 
-    files = sorted(glob(os.path.join(root, "**/*.tif"), recursive=True))
+    files = sorted(glob(os.path.join(root, f"**/*{file_ext}"), recursive=True))
+    # Raise an error if we could not find any files.
+    if len(files) == 0:
+        raise ValueError(f"Could not find any files in {root} with extension {file_ext}.")
+
     if metadata_file_name_pattern is None:
         metadata_files = [None] * len(files)
         offset = None
@@ -275,7 +314,7 @@ def convert_lightsheet_to_bdv(
                 recursive=True
             )
         )
-        assert len(metadata_files) == len(files)
+        assert len(metadata_files) == len(files), f"{len(metadata_files)}, {len(files)}"
 
         if center_tiles:
             start_positions = []
@@ -316,12 +355,7 @@ def convert_lightsheet_to_bdv(
             )
 
         print(f"Converting tp={timepoint}, channel={attributes['channel']}, tile={attributes['tile']}")
-        try:
-            data = tifffile.memmap(file_path, mode="r")
-        except ValueError:
-            print(f"Could not memmap the data from {file_path}. Fall back to load it into memory.")
-            data = tifffile.imread(file_path)
-
+        data = _load_data(file_path, metadata_file)
         if scale_factors is None:
             scale_factors = derive_scale_factors(data.shape)
 
@@ -337,6 +371,7 @@ def convert_lightsheet_to_bdv(
                 affine=tile_transformation,
                 timepoint=timepoint,
                 setup_id=setup_id,
+                chunks=(128, 128, 128),
             )
 
     # We don't need to add additional xml metadata if we convert to ome-zarr.

scripts/convert_raw_cochlea_sample.py

@@ -0,0 +1,13 @@
+from flamingo_tools.data_conversion import convert_lightsheet_to_bdv
+
+
+def main():
+    root = "/mnt/lustre-grete/usr/u12086/moser/lightsheet/M_LR_000172_R"
+    output = "/mnt/lustre-grete/usr/u12086/moser/lightsheet/M_LR_000172_R/converted.n5"
+    convert_lightsheet_to_bdv(
+        root, out_path=output, file_ext=".raw",
+        metadata_file_name_pattern="*_Settings.txt"
+    )
+
+
+main()

scripts/data_transfer/README.md

@@ -15,8 +15,7 @@ Current approach to the data transfer:
     - mget *
 - Copy this to HLRN by logging into it and running
   $ rsync  pape41:/scratch1/projects/cca/data/moser/<NAME>
-  $ rsync -e "ssh -i ~/.ssh/id_rsa_hlrn" -avz [email protected]:/scratch1/projects/cca/data/mose
-r/<NAME> /mnt/lustre-grete/usr/u12086/moser/lightsheet/<NAME>
+  $ rsync -e "ssh -i ~/.ssh/id_rsa_hlrn" -avz [email protected]:/scratch1/projects/cca/data/moser/<NAME> /mnt/lustre-grete/usr/u12086/moser/lightsheet/<NAME>
 - Remove on SCC
 
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