clears comments

src/main.py

@@ -174,57 +174,8 @@ def deduplicate_instruments_from_layers(layers):
         "deposition_chamber": ", ".join(ded_chambers),
         "rheed_system": ", ".join(ded_rheeds),
     }  # dictionary's name is a joke
-    # updated_dict = {} # use this for containing the final dataset
-    # for ded in elegant_dict:
-    #     if len(elegant_dict[ded]) == 0:
-    #         # if len of list is 0 - empty list - raise error
-    #         raise IndexError(f"Missing data: no Laser System, Chamber and/or RHEED System is specified in any of the Deposition-type experiments related to this sample. Fix this on eLabFTW before retrying. Affected list: {ded}.")
-    #     elif len(elegant_dict[ded]) > 1:
-    #         # if len of list is > 1 - too many values - allow the user to pick one
-    #         print("Warning: different instruments have been used for different layers - which is currently not allowed.")
-    #         # there's a better way to do this but I can't remember now for the life of me...
-    #         i = 0
-    #         while i < len(elegant_dict[ded]):
-    #             print(f"{i} - {elegant_dict[ded][i]}")
-    #             i += 1
-    #         ans = None
-    #         while not type(ans) == int or not ans in range(0, len(elegant_dict[ded])):
-    #             ans = input("Please pick one of the previous (0, 1, ...) [default = 0]: ") or "0"
-    #             if ans.isdigit():
-    #                 ans = int(ans)
-    #             continue # unnecessary?
-    #         updated_dict[ded] = elegant_dict[ded][ans]
-    #     elif elegant_dict[ded][0] in ["", 0, None]:
-    #         # if len is 1 BUT value is "", 0 or None raise error
-    #         raise ValueError(f"Missing data: a Laser System, Chamber and/or RHEED System which is specified across all the Deposition-type experiments related to this sample is either empty or invalid. Fix this on eLabFTW before retrying. Affected list: {ded}.")
-    #     else:
-    #         # if none of the previous (only 1 value), that single value is used
-    #         updated_dict[ded] = elegant_dict[ded][0]
-    # instruments_used_dict = {
-    #     "laser_system": updated_dict["Laser Systems"],
-    #     "deposition_chamber": updated_dict["Deposition Chamber"],
-    #     "rheed_system": updated_dict["RHEED Systems"],
-    # }
     return elegant_dict
 
-    ### OLD CODE
-    # if 0 in [ len(i) for i in elegant_list ]:
-    #     # i.e. if length of one of the lists in elegant_list is zero (missing data):
-    #     raise IndexError("Missing data: no Laser System, Chamber and/or RHEED System is specified in any of the Deposition-type experiments related to this sample.")
-    # if not all([ len(i) == 1 for i in elegant_list ]):
-    #     print("Warning: different instruments have been used for different layers - which is currently not allowed.")
-    #     # for every element in elegant list check if len > 1 and if it is
-    #     print("Selecting the first occurence for every category...")
-    ###
-    # lasers = { f"layer_{lyr.layer_number}": lyr.laser_system for lyr in layers }
-    # chambers = { f"layer_{lyr.layer_number}": lyr.deposition_chamber for lyr in layers }
-    # rheeds = { f"layer_{lyr.layer_number}": lyr.rheed_system for lyr in layers }
-    # instruments_used_dict = {
-    #     "laser_system": lasers,
-    #     "deposition_chamber": chambers,
-    #     "rheed_system": rheeds,
-    # }
-
 
 def select_rheed_data(layer):
     """
@@ -505,7 +456,17 @@ def make_nexus_schema_dictionary(substrate_object, layers):
     return pld_fabrication
 
 
-def build_nexus_file(pld_fabrication, output_path):
+def build_nexus_file(pld_fabrication, output_path="output/nffa-di_unnamed.h5"):
+    """
+    The function which actually builds the NeXus file for *PLD DEPOSITIONS*.
+    Saves the file in the specified directory.
+
+    Args:
+        pld_fabrication:
+        output_path:        The full path to the output file, including filename complete with extension.
+                            It's a string, which should be produced with os.path.
+                            Default value is: "output/nffa-di_unnamed.h5" - which is NOT NFFA-DI compliant.
+    """
     # NOTE: look at the mail attachment from Emiliano...
     with h5py.File(output_path, "w") as f:
         nx_pld_entry = f.create_group("pld_fabrication")
@@ -845,6 +806,7 @@ def build_nexus_file(pld_fabrication, output_path):
             if image_path and os.path.isfile(image_path):
                 img = Image.open(image_path).convert("L")
                 heatmap_matrix = np.array(img, dtype=np.uint8)  # or None
+                # heatmap_matrix = heatmap_matrix.astype(np.float32) / 255.0  # toggle to normalize matrix values
 
             if heatmap_matrix is not None:
                 heatmap = nx_rheed_layer.create_dataset(
@@ -874,21 +836,6 @@ def build_nexus_file(pld_fabrication, output_path):
     #   * Layer.fetch_textual_uploads() - dictionary
     #   * Layer.fetch_images() - dictionary
 
-    # nx_rheed = nx_pld_entry.create_group("rheed_data")
-    # nx_rheed.attrs["NX_class"] = "NXdata"
-
-    # nx_rheed.create_dataset("time", data=rheed_osc["time"])
-    # nx_rheed["time"].attrs["units"] = "s"
-
-    # nx_rheed.create_dataset("intensity", data=rheed_osc["intensity"])
-    # #nx_rheed["intensity"].attrs["units"] = "counts"
-    # nx_rheed["intensity"].attrs["long_name"] = "RHEED intensity"
-    # nx_rheed.attrs["signal"] = "intensity"
-    # nx_rheed.attrs["axes"] = "layer:time:channel"
-    # nx_rheed.attrs["layer_indices"] = [0]  # asse layer
-    # nx_rheed.attrs["time_indices"] = [1]   # asse tempo
-    # nx_rheed.attrs["channel_indices"] = [2]
-
 
 if __name__ == "__main__":
     # TO-DO: place the API base URL somewhere else.
@@ -907,7 +854,6 @@ if __name__ == "__main__":
     substrate_object = chain_entrypoint_to_batch(sample)  # Substrate-class object
     layers = chain_entrypoint_to_layers(sample)  # list of Layer-class objects
     n_layers = len(layers)  # total number of layers on the sample
-    result = make_nexus_schema_dictionary(substrate_object, layers)
     # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
     fn_base = (
         "nffa-di_"
@@ -916,17 +862,9 @@ if __name__ == "__main__":
         + "_"
         + sample_name
     )
+
+    result = make_nexus_schema_dictionary(substrate_object, layers)
     with open(f"output/{fn_base}.json", "w") as f:
         json.dump(result, f, indent=3)
-    # TO-DO: remove the hard-coded path of the RWA file
-    # ideally the script should download a TXT/CSV file from each layer
-    # (IF PRESENT ←→ also handle missing file error)
-    # and merge all data in a single file to analyse it
-    # WARNING: fails if file is missing
 
-    # This one tries to open a png image.
-    # Emiliano said to keep it to one image per layer tops.
-    # In this test I will only consider one image.
-    # TO-DO: make it format-agnostic. If not possible, make it PNG-only.
-    # mx = mx.astype(np.float32) / 255.0  # consider deleting???
     build_nexus_file(result, output_path=f"output/{fn_base}.h5")