Merge pull request #25 from dbouget/dynamic_plane_export

Dynamic plane export
andreped · Sep 11, 2024 · 444fe6e · 444fe6e
2 parents de92c1f + d35e683
commit 444fe6e
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Showing 2 changed files with 40 additions and 3 deletions.
diff --git a/vsi2tif/src/process.py b/vsi2tif/src/process.py
@@ -1,4 +1,7 @@
+import logging
 import os
+import shutil
+import traceback
 
 from tqdm import tqdm
 
@@ -18,7 +21,35 @@ def cellsens2tif_single(
     max_mem: int = 32,
     verbose: int = 1,
 ) -> None:
-    cellsens2tif(input_path, output_path, bfconvert, compression, tz, plane, quality, max_mem, verbose)
+
+    if int(plane) == -1:
+        image_folder = os.path.join(os.path.dirname(output_path), os.path.basename(output_path).replace(".tif", ""))
+        for s in range(50):
+            try:
+                curr_output_path = os.path.join(image_folder, "plane_" + str(s) + "_" + os.path.basename(output_path))
+                cellsens2tif(input_path, curr_output_path, bfconvert, compression, tz, s, quality, max_mem, verbose)
+            except Exception:
+                logging.info("End of planes with value {}".format(s))
+                break
+
+        try:
+            largest_size = 0
+            largest_file = None
+            for _, _, files in os.walk(image_folder):
+                for f in files:
+                    fp = os.path.join(image_folder, f)
+                    fs = os.path.getsize(fp)
+                    if fs > largest_size:
+                        largest_size = fs
+                        largest_file = fp
+            shutil.copyfile(largest_file, output_path)
+            if os.path.exists(image_folder):
+                shutil.rmtree(image_folder)
+        except Exception:
+            logging.error("Issue cleaning up after all planes conversion.")
+            logging.error(traceback.format_exc())
+    else:
+        cellsens2tif(input_path, output_path, bfconvert, compression, tz, plane, quality, max_mem, verbose)
 
 
 @benchmark
@@ -57,7 +88,7 @@ def cellsens2tif_batch(
             curr_output_path = (output_path + "/" + curr_input_path.split(input_path)[-1]).replace(".vsi", ".tif")
 
         try:
-            cellsens2tif(
+            cellsens2tif_single(
                 curr_input_path, curr_output_path, bfconvert, compression, tz, plane, quality, max_mem, verbose
             )
         except Exception:

diff --git a/vsi2tif/vsi2tif.py b/vsi2tif/vsi2tif.py
@@ -13,7 +13,13 @@ def main():
     parser.add_argument("-b", "--bfconvert", help="path to bfconvert tool", required=True)
     parser.add_argument("-c", "--compression", help="compression technique for final image", default="jpeg")
     parser.add_argument("-s", "--tilesize", help="tile size to use during both conversion steps", default=1024)
-    parser.add_argument("-p", "--plane", help="which image plane to convert image from", default=0)
+    parser.add_argument(
+        "-p",
+        "--plane",
+        help="which image plane to convert image from. If set to -1, all planes are converted and the largest is kept",
+        default=0,
+        type=int,
+    )
     parser.add_argument("-q", "--quality", help="compression quality used with JPEG compression", default=85)
     parser.add_argument("-m", "--max-mem", help="set maximum memory in the java vm", default=32)
     parser.add_argument("-v", "--verbose", help="set verbosity level", default=1, type=int)