minimal modifications

one method fetches all
one filters textual uploads
one filters png and bmp images

requirements.txt

@@ -2,3 +2,4 @@ requests
 asyncio
 h5py
 pillow
+elabapi_python

src/APIHandler.py

@@ -1,41 +1,150 @@
-import requests
+import os, requests
+import elabapi_python as elabapi
+
 
 class APIHandler:
-    '''
-    Class to standardize the format of the headers of our http requests.
-    '''
+    """
+    Class which handles all interactions with the eLabFTW API.
+    It provides methods to retrieve data from the API and download attachments.
+    It relies minimally on the elabapi-python library, which is used only for downloading attachments
+    (since the API doesn't support downloading attachments AFAIK).
+
+    Args:
+        api_key:          A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
+                          eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
+                          If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
+                          Or RTFM and create one yourself, it's not that hard.
+        ELABFTW_API_URL:  Complete URL of the eLabFTW instance's root for the API endpoints.
+                          In full caps because it won't (shouldn't) be changed much.
+    """
+
     # TO-DO: remove static url.
-    def __init__(self, apikey="", ELABFTW_API_URL="https://elabftw.fisica.unina.it/api/v2"):
-        '''Init method, apikey suggested but not required (empty by default).'''
-        self.auth = {"Authorization" : apikey}
-        self.content = {"Content-Type" : "application/json"}
+    def __init__(
+        self, api_key="", ELABFTW_API_URL="https://elabftw.fisica.unina.it/api/v2"
+    ):
+        """Init method, apikey suggested but not required (empty by default)."""
+        self.api_key = api_key
+        self.auth = {"Authorization": api_key}
+        self.content = {"Content-Type": "application/json"}
         self.header = {**self.auth, **self.content}
         self.elaburl = ELABFTW_API_URL
-    def get_entry_from_elabid(self, elabid, entryType="items"):
-        '''
-        Method which returns a resource's raw data (as dictionary) from its elabid and entry type.
 
-        Entry type can be either "experiments" or "items".
-        '''
-        # TO-DO: validation and error handling on entryType value.
+    def get_entry_from_elabid(self, elabid, entryType="items"):
+        """
+        Returns raw data (as dictionary) from its elabid and entry type.
+
+        args:
+            elabid:     elabftw internal id of the selected resource.
+            entryType:  Resource type. Anything other than "experiments" or "items" WILL raise an error.
+        """
+        if entryType not in ["experiments", "items"]:
+            raise Exception(
+                "You can only download attachments from experiments or items."
+            )
+
         header = self.header
         response = requests.get(
-            headers = header,
-            url = f"{self.elaburl}/{entryType}/{elabid}",
-            verify=True
+            headers=header, url=f"{self.elaburl}/{entryType}/{elabid}", verify=True
         )
-        if response.status_code // 100 in [1,2,3]:
+
+        # Response is 5xx = server error:
+        if response.status_code // 100 == 5:
+            raise ConnectionError(
+                f"There's a problem on the server. Status code: {response.status_code}."
+            )
+
+        # Response is 4xx = client error:
+        if response.status_code // 100 == 4:
+            match response.status_code:
+                case 401 | 403:
+                    # Forbidden or unauthorized:
+                    raise ConnectionError(
+                        f"Invalid API key, authentication method or elabid. Check if an item with ID = {elabid} actually exists."
+                    )
+                case 404:
+                    # Lapalissian:
+                    raise ConnectionError(
+                        f"404: Not Found. This means there's no resource with this elabid (wrong elabid?) on your eLabFTW (wrong endpoint?)."
+                    )
+                case 400:
+                    # I genuinely have no idea:
+                    raise ConnectionError(
+                        f"400: Bad Request. This means the API endpoint you tried to reach is invalid. Did you tamper with the source code? If not, contact the developer."
+                    )
+                case _:
+                    # For some fucking reason, this is the only error I actually get from the API...
+                    raise ConnectionError(
+                        f"HTTP request failed with status code: {response.status_code} (NOTE: 4xx means user's fault)."
+                    )
+
         entry_data = response.json()
         return entry_data
-        elif response.status_code // 100 == 4:
-            match response.status_code:
-                case 401|403:
-                    raise ConnectionError(f"Invalid API key, authentication method or elabid. Check if an item with ID = {elabid} actually exists.")
-                case 404:
-                    raise ConnectionError(f"404: Not Found. This means there's no resource with this elabid (wrong elabid?) on your eLabFTW (wrong endpoint?).")
-                case 400:
-                    raise ConnectionError(f"400: Bad Request. This means the API endpoint you tried to reach is invalid. Did you tamper with the source code? If not, contact the developer.")
-                case _:
-                    raise ConnectionError(f"HTTP request failed with status code: {response.status_code} (NOTE: 4xx means user's fault).")
-        else:
-            raise ConnectionError(f"There's a problem on the server. Status code: {response.status_code}.")
+
+    def download_attachments_data(self, elabid, entryType="experiments"):
+        """
+        Downloads attachments of a certain eLabFTW experiment (default) or item.
+        Only returns their binary data. Use method download_attachments_to_disk to save to file.
+        NOTE: Output is a dictionary where:
+            * The keys are the attachments' filenames;
+            * The values are the binary data for those attachments.
+
+        Args:
+            elabid:     eLabFTW internal ID of the selected resource.
+            entryType:  Resource type. Anything other than "experiments" or "items" WILL raise an error.
+        """
+        if entryType not in ["experiments", "items"]:
+            raise Exception(
+                "You can only download attachments from experiments or items."
+            )
+
+        config = elabapi.Configuration()
+        config.api_key["api_key"] = api_key
+        config.api_key_prefix["api_key"] = "Authorization"
+        config.host = self.elaburl
+        config.debug = False
+        api_client = elabapi.ApiClient(config)
+        api_client.set_default_header(
+            header_name="Authorization", header_value=self.api_key
+        )
+        uploads_api = elabapi.UploadsApi(api_client)
+
+        # Actual uploads (dictionary):
+        uploads = {
+            upload.real_name: uploads_api.read_upload(
+                entryType, elabid, upload.id, format="binary", _preload_content=False
+            ).data
+            for upload in uploads_api.read_uploads(entryType, elabid)
+        }
+
+        return uploads
+
+    def download_attachments_to_disk(
+        self,
+        elabid,
+        entryType="experiments",
+        dump_dir="output/attachments",
+        # persistent=True,
+    ):
+        """
+        Downloads attachments of a certain eLabFTW experiment (default) or item.
+        Downloads their binary data through method download_attachments_data and dumps it to dump_dir.
+
+        Args:
+            elabid:     eLabFTW internal ID of the selected resource.
+            entryType:  Resource type. Anything other than "experiments" or "items" WILL raise an error.
+            dump_dir:   Directory to which to save the attachments. Default is "output/attachments".
+            persistent: [Unused] Decides if the files will stay on disk after all operations are completed.
+                        If set to False, deletes the file upon exiting.
+        """
+
+        if entryType not in ["experiments", "items"]:
+            raise Exception(
+                "You can only download attachments from experiments or items."
+            )
+
+        uploads = download_attachments_data(elabid, entryType=entryType)
+        for file in uploads:
+            raw_data = uploads["file"]
+            with open(os.path.join(dump_dir, f"exp{elabid}-{file}"), "wb") as f:
+                f.write(raw_data)
+        return

src/classes.py

@@ -1,8 +1,9 @@
 import os, json, requests
 from APIHandler import APIHandler
 
+
 class Layer:
-    '''
+    """
     Layer(layer_data) - where layer_data is a Python dictionary.
 
     Meant to be used for eLabFTW Experiments of the "PLD Deposition" category.
@@ -10,12 +11,17 @@ class Layer:
     eLabFTW experiments contain most of the data required by the NeXus file - although every layer is on a different eLab entry;
     unfortunately, some data like the target's chemical formula must be retrieved through additional HTTP requests.
     Attributes 'target_elabid', 'rheed_system_elabid' and 'laser_system_elabid' contain elabid's for these resources, which are all items.
-    '''
+    """
+
     def __init__(self, layer_data):
         try:
+            self.elabid = layer_data["id"]
             self.operator = layer_data["fullname"]
             self.extra = layer_data["metadata_decoded"]["extra_fields"]
-            self.layer_number = self.extra["Layer Progressive Number"]["value"] # integer
+            self.uploads = layer_data["uploads"]  # dict
+            self.layer_number = self.extra["Layer Progressive Number"][
+                "value"
+            ]  # integer
             self.target_elabid = self.extra["Target"]["value"]  # elabid
             self.laser_system_elabid = self.extra["Laser System"]["value"]  # elabid
             self.chamber_elabid = self.extra["Chamber"]["value"]  # elabid
@@ -25,7 +31,9 @@ class Layer:
             self.repetition_rate = self.extra["Repetition rate"]["value"]
             self.repetition_rate_unit = self.extra["Repetition rate"]["unit"]
             try:
-                self.number_of_pulses = (float(self.deposition_time) * float(self.repetition_rate)).__floor__()
+                self.number_of_pulses = (
+                    float(self.deposition_time) * float(self.repetition_rate)
+                ).__floor__()
             except ValueError:
                 # Since number_of_pulses is required, if it can't be calculated raise error:
                 raise ValueError("""
@@ -33,22 +41,32 @@ class Layer:
     This has to be an error, since these fields are required by the NeXus standard.
     Please edit your eLabFTW entry and retry.
                 """)
-            self.temperature = self.extra["Heater temperature"]["value"] # Note: this field used to have a trailing space in its name
+            self.temperature = self.extra["Heater temperature"][
+                "value"
+            ]  # Note: this field used to have a trailing space in its name
             self.temperature_unit = self.extra["Heater temperature"]["unit"]
-            self.process_pressure = self.extra["Process pressure"]["value"] # Note: this field used to have a trailing space in its name
+            self.process_pressure = self.extra["Process pressure"][
+                "value"
+            ]  # Note: this field used to have a trailing space in its name
             self.process_pressure_unit = self.extra["Process pressure"]["unit"]
             self.heating_method = self.extra["Heating Method"]["value"]
             self.layer_thickness = self.extra["Thickness"]["value"]
             self.layer_thickness_unit = self.extra["Thickness"]["unit"]
             self.buffer_gas = self.extra["Buffer gas"]["value"]
             self.heater_target_distance = self.extra["Heater-target distance"]["value"]
-            self.heater_target_distance_unit = self.extra["Heater-target distance"]["unit"]
-            self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity
+            self.heater_target_distance_unit = self.extra["Heater-target distance"][
+                "unit"
+            ]
+            self.laser_fluence = self.extra["Laser Intensity"][
+                "value"
+            ]  # here fluence = intensity
             self.laser_fluence_unit = "J/(s cm^2)"
             self.laser_spot_area = self.extra["Spot Area"]["value"]
             self.laser_spot_area_unit = "mm^2"
             try:
-                self.laser_energy = ( float(self.laser_fluence) * float(self.laser_spot_area) / 100 ).__round__(3)
+                self.laser_energy = (
+                    float(self.laser_fluence) * float(self.laser_spot_area) / 100
+                ).__round__(3)
                 self.laser_energy_unit = "J/s"
             except ValueError:
                 # Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution:
@@ -61,39 +79,66 @@ class Layer:
                 self.laser_energy = "N/A"
                 self.laser_energy_unit = "J/s"
             # Laser rasternig section
-            self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"]["value"]
-            self.laser_rastering_positions = self.extra["Laser Rastering Position"]["value"]
-            self.laser_rastering_velocities = self.extra["Laser Rastering Speed"]["value"]
+            self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"][
+                "value"
+            ]
+            self.laser_rastering_positions = self.extra["Laser Rastering Position"][
+                "value"
+            ]
+            self.laser_rastering_velocities = self.extra["Laser Rastering Speed"][
+                "value"
+            ]
             # Pre annealing section
             self.pre_annealing_ambient_gas = self.extra["Buffer gas Pre"]["value"]
             self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"]
-            self.pre_annealing_temperature = self.extra["Heater temperature Pre"]["value"]
+            self.pre_annealing_temperature = self.extra["Heater temperature Pre"][
+                "value"
+            ]
             self.pre_annealing_duration = self.extra["Duration Pre"]["value"]
-            self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"]["unit"]
-            self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"]["unit"]
+            self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"][
+                "unit"
+            ]
+            self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"][
+                "unit"
+            ]
             self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"]
             # Post annealing section
             self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"]
             self.post_annealing_pressure = self.extra["Process pressure PA"]["value"]
-            self.post_annealing_temperature = self.extra["Heater temperature PA"]["value"]
+            self.post_annealing_temperature = self.extra["Heater temperature PA"][
+                "value"
+            ]
             self.post_annealing_duration = self.extra["Duration PA"]["value"]
-            self.post_annealing_pressure_unit = self.extra["Process pressure PA"]["unit"]
-            self.post_annealing_temperature_unit = self.extra["Heater temperature PA"]["unit"]
+            self.post_annealing_pressure_unit = self.extra["Process pressure PA"][
+                "unit"
+            ]
+            self.post_annealing_temperature_unit = self.extra["Heater temperature PA"][
+                "unit"
+            ]
             self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"]
 
             # Rejected but suggested by the NeXus standard:
-            #self.laser_rastering_coefficients = None
+            # self.laser_rastering_coefficients = None
         except KeyError as k:
             # Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
             # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the deposition layer entry on eLabFTW and make sure you used the correct Experiment template.")
+            raise KeyError(
+                f'The provided dictionary lacks a "{k}" key. Check the deposition layer entry on eLabFTW and make sure you used the correct Experiment template.'
+            )
         # Optional
         self.start_time = layer_data.get("created_at") or None
         self.description = layer_data.get("body") or None
-    def get_instruments(self, apikey):
-        raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(self.laser_system_elabid, entryType="items")
-        raw_chamber_data = APIHandler(apikey).get_entry_from_elabid(self.chamber_elabid, entryType="items")
-        raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid(self.rheed_system_elabid, entryType="items")
+
+    def get_instruments(self, api_key):
+        raw_lasersys_data = APIHandler(api_key).get_entry_from_elabid(
+            self.laser_system_elabid, entryType="items"
+        )
+        raw_chamber_data = APIHandler(api_key).get_entry_from_elabid(
+            self.chamber_elabid, entryType="items"
+        )
+        raw_rheedsys_data = APIHandler(api_key).get_entry_from_elabid(
+            self.rheed_system_elabid, entryType="items"
+        )
         instruments_used = {
             "laser_system": raw_lasersys_data.get("title") or None,
             "deposition_chamber": raw_chamber_data.get("title") or None,
@@ -101,31 +146,96 @@ class Layer:
         }
         return instruments_used
 
+    def list_attachments(self):
+        """
+        Returns a dictionary of all the attachments linked to the layer, where:
+            * Each key is the attachment's elabid;
+            * Each value is a dictionary containing the attachment's filename, hashname and related experiment elabid (= self.elabid).
+
+        Data is already in layer_data, so the API key is unrequired. Same goes for:
+            * fetch_textual_uploads() - no arguments;
+            * fetch_images() - no arguments.
+        """
+        # Remember: Layers are experiments, so we only need to look for attachments in the experiment endpoint.
+        attachments = {
+            attachment["id"]: {
+                "filename": attachment["real_name"],
+                "hashname": attachment["long_name"],
+                "related_experiment": attachment["item_id"],
+            }
+            for attachment in self.uploads
+        }
+        return attachments
+
+    def fetch_textual_uploads(self):
+        """
+        Starting from the list of attachments, filters out and returns a list of the textual uploads linked to the layer, which can be either plain text, csv, tsv etc.
+        Returns only their names, so that the user may select which one to import into the NeXus file as a dataset.
+
+        It only looks for .txt, .csv and .tsv files, although it could be easily modified to include other formats.
+        It is also file extension-sensitive, so anything not ending with .txt, .csv or .tsv won't be retrieved.
+        That's because the API (v5.3.11) doesn't provide MIME Type or similar metadata on the attachments, so the only way to know if an attachment is an image or not is through its filename.
+        """
+        attachments = self.list_attachments()
+        textual_uploads = {
+            attachment: attachments[attachment]
+            for attachment in attachments
+            if attachments[attachments]["filename"][-4:] in (".txt", ".csv", ".tsv")
+        }
+        return textual_uploads
+
+    def fetch_images(self):
+        """
+        Starting from the list of attachments, filters out and returns a Starting from the list of attachments, filters out and returns a list of all the (PNG or BMP) images attached to the layer.
+        Hopefully one of them is a RHEED pattern.
+        Returns only their names, so that the user may select which one to import into the NeXus file as a RHEED acquisition.
+
+        It only looks for .png and .bmp files, although it could be easily modified to include other formats.
+        It is also file extension-sensitive, so anything not ending with .png or .bmp won't be retrieved, even if it's an actual image.
+        That's because the API (v5.3.11) doesn't provide MIME Type or similar metadata on the attachments, so the only way to know if an attachment is an image or not is through its filename.
+        """
+        attachments = self.list_attachments()
+        pictures = {
+            attachment: attachments[attachment]
+            for attachment in attachments
+            if attachments[attachments]["filename"][-4:] in (".png", ".bmp")
+        }
+        return pictures
+
+
 class Entrypoint:
-    '''
+    """
     Entrypoint(sample_data) - where sample_data is a Python dictionary.
 
     Meant to be used for eLabFTW Resources of the "Sample" category.
 
     The entrypoint is the starting point of the process of resolving the data chain.
     The entrypoint must be a dictionary containing the data of a sample, created directly from the JSON of the item endpoint on eLabFTW - which can be done through the function get_entry_from_elabid.
-    '''
+    """
+
     def __init__(self, sample_data):
         try:
             self.extra = sample_data["metadata_decoded"]["extra_fields"]
             self.linked_items = sample_data["items_links"]  # dict
             self.batch_elabid = self.extra["Substrate batch"]["value"]  # elabid
             self.linked_experiments = sample_data["related_experiments_links"]  # dict
-            self.linked_experiments_elabid = [ i["entityid"] for i in self.linked_experiments ] # list of elabid
+            self.linked_experiments_elabid = [
+                i["entityid"] for i in self.linked_experiments
+            ]  # list of elabid
         except KeyError as k:
             # Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
             # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the sample entry on eLabFTW and make sure you used the correct Resource template.")
+            raise KeyError(
+                f'The provided dictionary lacks a "{k}" key. Check the sample entry on eLabFTW and make sure you used the correct Resource template.'
+            )
         # Non-required attributes:
-        self.name = sample_data.get("title") or None # error prevention is more important than preventing empty fields here
+        self.name = (
+            sample_data.get("title") or None
+        )  # error prevention is more important than preventing empty fields here
+
 
 class Material:
-    '''
+    """
     Material(material_data) - where material_data is a Python dictionary.
 
     Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories.
@@ -134,13 +244,16 @@ class Material:
         * Name and formula;
         * Shape and dimensions;
         * Misc.
-    '''
+    """
+
     def __init__(self, material_data):
         try:
             self.name = material_data["title"]  # required
             self.extra = material_data["metadata_decoded"]["extra_fields"]
             self.compound_elabid = self.extra["Compound"]["value"]
-            self.dimensions = str(self.extra["Size"]["value"]) # strings have a .count() method
+            self.dimensions = str(
+                self.extra["Size"]["value"]
+            )  # strings have a .count() method
             if self.dimensions.count("mm") == 2:
                 self.dimensions_unit = "mm x mm"
             elif self.dimensions[-1] == '"':
@@ -150,23 +263,30 @@ class Material:
         except KeyError as k:
             # Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
             # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the target/substrate entry on eLabFTW and make sure you used the correct Resource template.")
+            raise KeyError(
+                f'The provided dictionary lacks a "{k}" key. Check the target/substrate entry on eLabFTW and make sure you used the correct Resource template.'
+            )
+
     def get_compound_data(self, apikey):
-        raw_compound_data = APIHandler(apikey).get_entry_from_elabid(self.compound_elabid, entryType="items")
+        raw_compound_data = APIHandler(apikey).get_entry_from_elabid(
+            self.compound_elabid, entryType="items"
+        )
         name = raw_compound_data["title"]
         extra = raw_compound_data["metadata_decoded"]["extra_fields"]
         formula = extra.get("Chemical formula")
-        cas = extra.get("CAS number ") or { "value": None }
+        cas = extra.get("CAS number ") or {"value": None}
         compound_data = {
-            "name" : name,
-            "chemical_formula" : formula.get("value"),
-            "cas_number" : cas.get("value")
+            "name": name,
+            "chemical_formula": formula.get("value"),
+            "cas_number": cas.get("value"),
         }
         return compound_data
+
     def get_compound_formula(self, apikey):
         formula = self.get_compound_data(apikey).get("chemical_formula")
         return formula
 
+
 class Substrate(Material):
     def __init__(self, material_data):
         super().__init__(material_data)
@@ -176,13 +296,16 @@ class Substrate(Material):
             self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"]
             self.miscut_direction = self.extra["Miscut Direction"]["value"]
             # Not present (yet) on eLabFTW for Substrates:
-            self.thickness = "" #self.extra["Thickness"]["value"]
-            self.thickness_unit = "μm" #self.extra["Thickness"]["unit"]
+            self.thickness = ""  # self.extra["Thickness"]["value"]
+            self.thickness_unit = "μm"  # self.extra["Thickness"]["unit"]
             self.surface_treatment = self.extra["Surface treatment"]["value"]
             self.manufacturer = self.extra["Supplier"]["value"]
             self.batch_id = self.extra["Batch ID"]["value"]
         except KeyError as k:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for substrates. Check the {self.name} substrate entry on eLabFTW and make sure you used the correct Resource template.")
+            raise KeyError(
+                f'The provided dictionary lacks a "{k}" key - which is specific for substrates. Check the {self.name} substrate entry on eLabFTW and make sure you used the correct Resource template.'
+            )
+
 
 class Target(Material):
     def __init__(self, material_data):
@@ -194,13 +317,14 @@ class Target(Material):
             self.solid_form = self.extra["Solid form"]["value"]
             self.manufacturer = self.extra["Supplier"]["value"]
         except KeyError as k:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for PLD targets. Check the {self.name} target entry on eLabFTW and make sure you used the correct Resource template.")
+            raise KeyError(
+                f'The provided dictionary lacks a "{k}" key - which is specific for PLD targets. Check the {self.name} target entry on eLabFTW and make sure you used the correct Resource template.'
+            )
         # Non-required attributes:
         self.description = material_data.get("body") or ""
 
 
-
-if __name__=="__main__":
-    head = Header("MyApiKey-123456789abcdef")
+if __name__ == "__main__":
+    head = APIHandler("MyApiKey-123456789abcdef")
     print(f"Example header:\n\t{head.header}\n")
     print("Warning: you're not supposed to be running this as the main program.")

src/main.py

@@ -1,9 +1,11 @@
+#!/usr/bin/env python3
 import os, json, requests, h5py
 import numpy as np
 from getpass import getpass
 from APIHandler import APIHandler
 from classes import *
 from PIL import Image
+# from schema import pld_deposition
 
 
 def call_entrypoint_from_elabid(elabid):
@@ -212,10 +214,10 @@ def analyse_rheed_data(data):
     -----
 
     Distinct ValueErrors are raised if:
-    - The array is not 2-dimensional;
-    - The total number of columns does not equate exactly 1+3 (= 4).
+    * The array is not 2-dimensional;
+    * The total number of columns does not equate exactly 1+3 (= 4).
 
-    Time is expressed in seconds, intensities are normalized (adimensional).
+    Time is expressed in seconds, intensities are adimensional on 8 bits (min. 0, max. 255).
 
     # TO-DO: complete this description...
     Written with help from DeepSeek.
@@ -245,8 +247,8 @@ def analyse_rheed_data(data):
     intensities = data[:, 1:4].astype(np.float32, copy=False)
 
     return {
-        "time": time,
-        "intensity": intensities,
+        "time": np.transpose(time),
+        "intensity": np.transpose(intensities),
     }
 
 
@@ -715,6 +717,7 @@ if __name__ == "__main__":
     # (IF PRESENT ←→ also handle missing file error)
     # and merge all data in a single file to analyse it
     # WARNING: fails if file is missing
+
     with open("tests/Realtime_Window_Analysis.txt", "r") as o:
         osc = np.loadtxt(o, delimiter="\t")
     try:

src/schema/pld_deposition.py

@@ -0,0 +1,3 @@
+class Prova:
+    def __init__(self):
+        self.hello = "Hello world"