Merge pull request #26 from nemocrys/dev-nomdad

Nomad: add parent ELN file

multilog/devices/basler_camera.py

@@ -103,9 +103,9 @@ def init_output(self, directory="./"):
             f.write("time_abs,time_rel,img-name,\n")
         with open(f"{self.directory}/device.txt", "w", encoding="utf-8") as f:
             f.write(self.device_name)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:

multilog/devices/daq6510.py

@@ -264,15 +264,15 @@ def init_output(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/devices/eurotherm.py

@@ -91,15 +91,15 @@ def init_output(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/devices/ifm_flowmeter.py

@@ -167,15 +167,15 @@ def init_output(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/devices/optris_ip640.py

@@ -136,9 +136,9 @@ def init_output(self, directory="./"):
         with open(f"{self.directory}/_images.csv", "w", encoding="utf-8") as f:
             f.write("# datetime,s,filename,\n")
             f.write("time_abs,time_rel,img-name,\n")
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:

multilog/devices/process_condition_logger.py

@@ -73,15 +73,15 @@ def init_output(self, directory="./"):
                     f"- {condition}: {self.meas_data[condition]} {self.condition_units[condition]}\n"
                 )
             f.write("\n## Process condition log\n\n")
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/devices/pyrometer_array_lumasense.py

@@ -130,15 +130,15 @@ def init_output(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/devices/pyrometer_lumasense.py

@@ -149,15 +149,15 @@ def init_output(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
-        self.write_nomad_files(directory)
+        self.write_nomad_file(directory)
 
-    def write_nomad_files(self, directory="./"):
+    def write_nomad_file(self, directory="./"):
         """Write .archive.yaml file based on device configuration.
 
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
-        with open("./multilog/nomad/archive_template.yml") as f:
+        with open("./multilog/nomad/archive_template_sensor.yml") as f:
             nomad_template = yaml.safe_load(f)
         definitions = nomad_template.pop("definitions")
         data = nomad_template.pop("data")

multilog/main.py

@@ -1,6 +1,7 @@
 """This module contains the controller-part of multilog. It sets up the
 communication between device and visualization and manages the sampling
 loop."""
+from copy import deepcopy
 import shutil
 from PyQt5.QtWidgets import QApplication
 from PyQt5.QtCore import QTimer, QThread, QObject, pyqtSignal
@@ -293,13 +294,73 @@ def init_output_files(self):
                 break
         for device in self.devices:
             self.devices[device].init_output(self.directory)
+        self.write_nomad_file()
         self.write_metadata()
         shutil.copy(
             "./multilog/nomad/base_classes.schema.archive.yaml",
             f"{self.directory}/base_classes.schema.archive.yaml",
         )
         self.main_window.set_output_directory(self.directory)
 
+    def write_nomad_file(self):
+        """Write main multilog.archive.yaml including an overview of all devices."""
+        with open("./multilog/nomad/archive_template_main.yml") as f:
+            nomad_dict = yaml.safe_load(f)
+        data = nomad_dict.pop("data")
+        multilog_version = (
+            subprocess.check_output(
+                ["git", "describe", "--tags", "--dirty", "--always"]
+            )
+            .strip()
+            .decode("utf-8")
+        )
+        data["process"]["start_time"] = datetime.datetime.now(datetime.timezone.utc).astimezone().isoformat(timespec='milliseconds').replace('T', ' ')
+        data["data_processing"].update(
+            {
+                "software": f"multilog {multilog_version}",
+                "sampling_time": self.config["settings"]["dt-main"],
+                "image_time": self.config["settings"]["dt-camera"],
+            }
+        )
+
+        template_ir_cam = nomad_dict.pop("instrumentation_IR-camera_template")
+        template_camera = nomad_dict.pop("instrumentation_camera_template")
+        template_sensor = nomad_dict.pop("instrumentation_sensors_template")
+        for device_name in self.devices:
+            nomad_name = device_name.replace(" ", "_").replace("-", "_")
+            if "Optris-IP-640" in device_name:
+                instrument = deepcopy(template_ir_cam)
+                instrument["section"]["quantities"]["ir_camera"]["type"] = f"../upload/raw/{device_name}.archive.yaml#IR_camera"
+                nomad_dict["definitions"]["sections"]["MeltCzochralski"]["sub_sections"]["instrumentation"]["section"]["sub_sections"].update(
+                    {nomad_name: instrument}
+                )
+                data["instrumentation"][nomad_name] = {
+                    "ir_camera": f"../upload/raw/{device_name}.archive.yaml#data"
+                }
+            elif "Basler" in device_name:
+                instrument = deepcopy(template_camera)
+                instrument["section"]["quantities"]["camera"]["type"] = f"../upload/raw/{device_name}.archive.yaml#camera"
+                nomad_dict["definitions"]["sections"]["MeltCzochralski"]["sub_sections"]["instrumentation"]["section"]["sub_sections"].update(
+                    {nomad_name: instrument}
+                )
+                data["instrumentation"][nomad_name] = {
+                    "camera": f"../upload/raw/{device_name}.archive.yaml#data"
+                }
+            else:
+                instrument = deepcopy(template_sensor)
+                instrument["section"]["quantities"]["sensors_list"]["type"] = f"../upload/raw/{device_name}.archive.yaml#Sensors_list"
+                nomad_dict["definitions"]["sections"]["MeltCzochralski"]["sub_sections"]["instrumentation"]["section"]["sub_sections"].update(
+                    {nomad_name: instrument}
+                )
+                data["instrumentation"][nomad_name] = {
+                    "sensors_list": f"../upload/raw/{device_name}.archive.yaml#data"
+                }
+
+            nomad_dict.update({"data": data})
+            with open(f"{self.directory}/multilog_eln.archive.yaml", "w", encoding="utf-8") as f:
+                yaml.safe_dump(nomad_dict, f, sort_keys=False)
+
+
     def write_metadata(self):
         """Write a csv file with information about multilog version,
         python version and operating system.

multilog/nomad/archive_template_Camera.yml

@@ -1,3 +1,6 @@
+# NOMAD template for optical camera, based on
+# https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas/blob/main/melt_czochralski_Dadzis/IRcameras.archive.yaml
+
 definitions:
   name: 'Optical camera data'
   sections:

multilog/nomad/archive_template_IR-Camera.yml

@@ -1,3 +1,6 @@
+# NOMAD template for IR camera, based on
+# https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas/blob/main/melt_czochralski_Dadzis/IRcameras.archive.yaml
+
 definitions:
   name: 'IR camera data'
   sections: