Update file maxwell_integrate_to_h5.py

maxwell_integrate_to_h5.py

@@ -181,7 +181,7 @@ def integrate_ims_in_dir(path_im, path_int, dtype_im=".tif", dtype_int=".dat"):
             # Use a lambda function to pass the subdir_path_int to the integration_thread
             # Map async allows us to run the integration in parallel, with trace back of varibles
             async_result = pool.map_async(
-                            lambda fname_im: integration_thread(fname_im, subdir_path_int),
+                            lambda fname_im: integration_thread(fname_im),
                             filtered_fnames
                         )
 
@@ -261,10 +261,7 @@ def integrate_ims_in_dir(path_im, path_int, dtype_im=".tif", dtype_int=".dat"):
                 for idx, result in enumerate(results_data, start=1):
                     
                     # Drop unfinished scans (usually last scan due to closed shutter)
-                    if not result["q"].size or not result["I"].size:
-                        print(f"Skipping invalid scan data for entry {entry_name}")
-                        continue
-                    
+                    try:
                         # Here one could use the image sequence number from the metadata, however, we use the index as it seemes cleaner
                         entry_name = f"{idx:05d}.1"
                         
@@ -273,8 +270,6 @@ def integrate_ims_in_dir(path_im, path_int, dtype_im=".tif", dtype_int=".dat"):
                         entry["title"] = "Collected Q-I scans"
                         entry.attrs["NX_class"] = "NXentry"
                         
-
-                    
                         # Set time attributes for the entry	
                         entry.create_dataset("time", data=results_metadata[idx-1]["dateString"].encode('utf-8'), dtype=h5py.string_dtype(encoding='utf-8'))
                         
@@ -376,6 +371,10 @@ def integrate_ims_in_dir(path_im, path_int, dtype_im=".tif", dtype_int=".dat"):
                         if idx == len(results_data):  # mark the last one as global default
                             entry["last_plot"] = h5py.SoftLink(f"/{subdir_name}/{entry_name}/measurement")
                             
+                    except Exception as e:
+                        print(f"Error processing file {result['filename']}: {e}")
+                        continue
+                    
 
             print(f"✅ HDF5 file '{output_file}' created with {len(results_data)} spectra.")