adds new function to analyze rheed data, doesn't really work atm

thanks DeepSeek

src/main.py

@@ -179,6 +179,57 @@ def deduplicate_instruments_from_layers(layers):
     #     "rheed_system": rheeds,
     # }
 
+def analyse_rheed_data(data, n_layers: int):
+    '''
+    Takes the content of a tsv file and returns a dictionary with timestamps and intensities.
+    The file should contain a 2D array composed of 3N+1 columns - where N is the total number of layers in a given sample - and an unspecified number of rows.
+    
+    -----
+    Time    Layer1_Int1     Layer1_Int2     Layer1_Int3     (repeat...)
+    -----
+
+    Distinct ValueErrors are raised if:
+    - The array is not 2-dimensional;
+    - The number of (intensity) columns is not a multiple of 3;
+    - The total number of columns does not equate exactly 3N+1.
+
+    # TO-DO: complete this description...
+    Written with help from DeepSeek.
+    '''
+    # Verifying the format of the input file:
+    if data.ndim != 2:
+        raise ValueError(f"Unexpected trace format: expected 2D array, got ndim = {data.ndim}.")
+    n_cols = data.shape[1] # 0 = rows, 1 = columns
+    if (n_cols - 1) % 3 != 0:
+        raise ValueError(f"Unexpected number of columns: expected 3N+1 columns, got {n_cols}.")
+    if (n_cols - 1) // 3 != n_layers:
+        exp = n_layers * 3 + 1
+        raise ValueError(f"Unexpected volume of data: found {n_layers} layers, expected {exp} (3N+1) columns, got {n_cols}.")
+    n_time_points = data.shape[0]
+
+    # Get time (all rows of col 0) as Float64:
+    time = data[:, 0].astype(np.float64, copy=False) # copy=False suggested by LLM for mem. eff.
+
+    # Empty 3D array for intensities:
+    intensities = np.zeros(
+        (n_layers, n_time_points, 3)
+    )
+
+    # Loop through layers:
+    for layer_index in range(n_layers):
+        layer_name = f"layer_{layer_index + 1}"
+        # Columns for this layer are from 3i+1 to 3i+3 incl. (= 3i+4 excl.)
+        start_col = 1 + layer_index * 3
+        end_col = start_col + 3 # remember this gets excluded!
+        # Get layer-specific intensities (all rows of columns start_col:end_col) as Float32:
+        intensities[layer_index, :, :] = data[:, start_col:end_col].astype(np.float32, copy=False)
+
+    return {
+        "time": time,
+        "intensity": intensities,
+    }
+
+
 def make_nexus_schema_dictionary(substrate_object, layers):
     '''
     Main function, takes all the other functions to reconstruct the full dataset. Takes a Substrate-class object (output of the chain_entrypoint_to_batch() function) and a list of Layer-class objects (output of the chain_entrypoint_to_layers() function), returns dictionary with the same schema as the NeXus standard for PLD fabrications.
@@ -457,9 +508,23 @@ def build_nexus_file(pld_fabrication, output_path, rheed_osc=None):
             nx_instruments.create_dataset("rheed_system", data = instruments_dict["rheed_system"])
         except TypeError as te:
             raise TypeError(te)
-        nx_rheed = nx_pld_entry.create_group("rheed_data")
+        
-        nx_rheed.attrs["NX_class"] = "NXdata"
+        # RHEED data section
-        nx_rheed.create_dataset("intensity", data=rheed_osc)
+        if rheed_osc is not None:
+            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]
     return
 
 if __name__=="__main__":
@@ -472,10 +537,16 @@ if __name__=="__main__":
     sample_name = sample.name.strip().replace(" ","_")
     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
     with open (f"output/sample-{sample_name}.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
     with open(f"tests/Realtime_Window_Analysis.txt", "r") as o:
-        osc = np.loadtxt(o)
+        osc = np.loadtxt(o, delimiter="\t")
-    build_nexus_file(result, output_path=f"output/sample-{sample_name}-nexus.h5", rheed_osc=osc)
+    rheed_osc = analyse_rheed_data(data=osc, n_layers=n_layers) or None # analyze rheed data first, build the file later
+    build_nexus_file(result, output_path=f"output/sample-{sample_name}-nexus.h5", rheed_osc=rheed_osc)