Added dummy python copying file

pycromanager_step_1.py

@@ -0,0 +1,140 @@
+import os
+import sys
+import shutil
+import glob
+
+# Function to log messages
+def log_message(message):
+    with open('D:/log.txt', 'a') as log_file:
+        print(message, file=log_file, flush=True)
+
+def copy_tif_files(projectsFolderPath, sampleLabel, imageType):
+
+    if "4x" in imageType:
+        TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/BurnTest2-4x-bf'
+    else:
+        TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/PDAC.3.A_Unstained-20x--C-7'
+
+    log_message(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
+
+    dest_dir = os.path.join(projectsFolderPath, sampleLabel, imageType)
+    log_message(f"Destination directory: {dest_dir}")
+    if not os.path.exists(dest_dir):
+        log_message("Destination directory does not exist, creating it.")
+        os.makedirs(dest_dir)
+
+    tif_files = []
+    for extension in ['*.tif', '*.tiff', '*.txt']:
+        tif_files.extend(glob.glob(os.path.join(TILES_LOCATION, extension)))
+
+    log_message(f"Number of .tif files found: {len(tif_files)}")
+    if not tif_files:
+        log_message(f"No .tif files found in {TILES_LOCATION}")
+        return False
+
+    for file in tif_files:
+        try:
+            log_message(file)
+            shutil.copy(file, dest_dir)
+        except Exception as e:
+            print(f"Error copying file {file}: {e}")
+
+
+    return True
+
+log_message("Python script started.")
+projectsFolderPath = sys.argv[2]
+log_message(f"Projects Folder Path: {projectsFolderPath}")
+sampleLabel = sys.argv[3]
+log_message(f"Sample Label: {sampleLabel}")
+imageType = sys.argv[4]
+log_message(f"Image Type: {imageType}")
+
+success = copy_tif_files(projectsFolderPath, sampleLabel, imageType)
+
+if not success:
+    log_message("File copying did not complete successfully.")
+else:
+    log_message("File copying completed successfully.")
+
+
+# import os
+# import sys
+# import shutil
+# import glob
+
+# # Redirecting print statements to a log file
+# sys.stdout = open('logpython.txt', 'w')
+# print(os.getcwd())
+# def copy_tif_files(projectsFolderPath, sampleLabel, imageType):
+
+#     if "4x" in imageType:
+#         TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/BurnTest2-4x-bf'  # Replace with the absolute path
+#     else:
+#         TILES_LOCATION = 'C:/ImageAnalysis/Brightfield demo/Tiles/PDAC_MetroHealth_N352L42-20x--null'
+
+
+#     print(f"Copying .tif files from {TILES_LOCATION} to {projectsFolderPath}/{sampleLabel}")
+
+#     dest_dir = os.path.join(projectsFolderPath, sampleLabel, f"{imageType}{sampleLabel}")
+#     print(f"Destination directory: {dest_dir}")
+#     if not os.path.exists(dest_dir):
+#         print("Destination directory does not exist, creating it.")
+#         os.makedirs(dest_dir)
+
+#     # Find all .tif files
+#     tif_files = []
+#     for extension in ['*.tif', '*.tiff', '*.txt']:
+#         tif_files.extend(glob.glob(os.path.join(TILES_LOCATION, extension)))
+
+#     print(f"Number of .tif files found: {len(tif_files)}")
+#     #print(f"Files: {tif_files}")
+#     # Check if any.tif files were found
+#     if not tif_files:
+#         print(f"No .tif files found in {TILES_LOCATION}")
+#         return False
+#     #Copy each .tif file
+#     #shutil.copy(tif_files[0], dest_dir)
+#     # print(f"Copying last file: {tif_files[-1]}")
+#     # shutil.copy(tif_files[-1], dest_dir)
+
+#     # for file in tif_files[:42]:
+#     #     print(f"Copying file: {file}")
+#     #     shutil.copy(file, dest_dir)
+
+#     for file in tif_files:
+#         try:
+#             print(f"Copying file: {file}")
+#             shutil.copy(file, dest_dir)
+#         except Exception as e:
+#             print(f"Error copying file {file}: {e}")
+
+#     # print("Copy operation completed.")
+#     return True
+
+
+# # if len(sys.argv) != 9:
+# #     print("Incorrect arguments for function: python script.py <projectsFolderPath> <sampleLabel> <imageType> <x1> <y1> <x2> <y2>")
+# #     print(len(sys.argv))
+# #     return
+# print("Python script started.")
+# projectsFolderPath = sys.argv[2]
+# print(f"Projects Folder Path: {projectsFolderPath}")
+# sampleLabel = sys.argv[3]
+# print(f"Sample Label: {sampleLabel}")
+# imageType = sys.argv[4]
+# print(f"Image Type: {imageType}")
+# # x1, y1, x2, y2 are received but not used in this script. They can be used if needed.
+
+# #jsonFileLocation = sys.arv[9]
+# #WOULD NEED FUNCTION HERE TO TRANSLATE COORDINATES TO STAGE COORDINATES
+
+# success = copy_tif_files(projectsFolderPath, sampleLabel, imageType)
+
+# if not success:
+#     print("File copying did not complete successfully.")
+# else:
+#     print("File copying completed successfully.")
+
+# # Close the log file
+# sys.stdout.close()