Merge pull request #25 from nemocrys/dev-nomdad

Implement nomad support for remaining devices

Author: arvedes

multilog/devices/basler_camera.py

@@ -1,6 +1,7 @@
 import datetime
 import logging
 import os
+import shutil
 
 
 logger = logging.getLogger(__name__)
@@ -25,6 +26,7 @@ def __init__(self, config, name="BaslerCamera"):
                 config.yml in the devices-section).
             name (str, optional): Device name.
         """
+        self.config = config
         logger.info(f"Initializing BaslerCamera device '{name}'")
         self.name = name
         self._timeout = config["timeout"]
@@ -93,13 +95,29 @@ def init_output(self, directory="./"):
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
+        self.base_directory = directory
         self.directory = f"{directory}/{self.name}"
         os.makedirs(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")
         with open(f"{self.directory}/device.txt", "w", encoding="utf-8") as f:
             f.write(self.device_name)
+        self.write_nomad_files(directory)
+
+    def write_nomad_files(self, directory="./"):
+        """Write .archive.yaml file based on device configuration.
+
+        Args:
+            directory (str, optional): Output directory. Defaults to "./".
+        """
+        shutil.copy(
+            "./multilog/nomad/archive_template_Camera.yml",
+            f"{directory}/{self.name}.archive.yaml",
+        )
+        with open(f"{self.base_directory}/{self.name}.archive.yaml", "a") as f:
+            f.write(f"  exposure_time: {self.config['exposure-time']}\n")
+            f.write(f"  images_list:\n")
 
     def save_measurement(self, time_abs, time_rel, sampling):
         """Write measurement data to files:
@@ -125,6 +143,13 @@ def save_measurement(self, time_abs, time_rel, sampling):
             f.write(
                 f"{time_abs.isoformat(timespec='milliseconds').replace('T', ' ')},{time_rel},{img_name},\n"
             )
+        with open(f"{self.base_directory}/{self.name}.archive.yaml", "a") as f:  # todo
+            f.write(f"  - name: {img_name}\n")
+            f.write(f"    image: {self.name}/{img_name}\n")
+            f.write(f"    timestamp_rel: {time_rel}\n")
+            f.write(
+                f"    timestamp_abs: {time_abs.isoformat(timespec='milliseconds').replace('T', ' ')}\n"
+            )
         self.image_counter += 1
 
     def set_frame_rate(self, frame_rate):

multilog/devices/optris_ip640.py

@@ -4,8 +4,10 @@
 import multiprocessing
 import numpy as np
 import os
+import shutil
 import traceback
 
+
 logger = logging.getLogger(__name__)
 try:
     from ..pyOptris import direct_binding as optris
@@ -30,6 +32,7 @@ def __init__(self, config, name="OptrisIP640", xml_dir="./"):
             xml_dir(str, optional): Directory for xml-file with device
                 configuration. Defaults to "./".
         """
+        self.config = config
         logger.info(f"Initializing OptrisIP640 device '{name}'")
         self.name = name
         self.emissivity = config["emissivity"]
@@ -127,11 +130,31 @@ def init_output(self, directory="./"):
         Args:
             directory (str, optional): Output directory. Defaults to "./".
         """
+        self.base_directory = directory
         self.directory = f"{directory}/{self.name}"
         os.makedirs(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)
+
+    def write_nomad_files(self, directory="./"):
+        """Write .archive.yaml file based on device configuration.
+
+        Args:
+            directory (str, optional): Output directory. Defaults to "./".
+        """
+        shutil.copy(
+            "./multilog/nomad/archive_template_IR-Camera.yml",
+            f"{directory}/{self.name}.archive.yaml",
+        )
+        with open(f"{self.base_directory}/{self.name}.archive.yaml", "a") as f:
+            f.write(f"  emissivity: {self.emissivity}\n")
+            f.write(f"  transmissivity: {self.transmissivity}\n")
+            f.write(f"  ambient_temperature: {self.t_ambient}\n")
+            f.write(f"  measurement_range: '{self.config['measurement-range']}'\n")
+            f.write(f"  extended_temperature_range: {self.config['extended-T-range']}\n")
+            f.write(f"  ir_images_list:\n")
 
     def save_measurement(self, time_abs, time_rel, sampling):
         """Write measurement data to files:
@@ -164,9 +187,18 @@ def save_measurement(self, time_abs, time_rel, sampling):
             f.write(
                 f"{time_abs.isoformat(timespec='milliseconds').replace('T', ' ')},{time_rel},{img_name},\n"
             )
+        with open(f"{self.base_directory}/{self.name}.archive.yaml", "a") as f:
+            f.write(f"  - name: {img_name}\n")
+            f.write(f"    image: {self.name}/{img_name}.png\n")
+            f.write(f"    heat_map: {self.name}/{img_name}.csv\n")
+            f.write(f"    timestamp_rel: {time_rel}\n")
+            f.write(
+                f"    timestamp_abs: {time_abs.isoformat(timespec='milliseconds').replace('T', ' ')}\n"
+            )
+
         self.image_counter += 1
 
     def __del__(self):
-        """Terminate IR camera communictation and remove xml."""
+        """Terminate IR camera communication and remove xml."""
         optris.terminate()
         os.remove(self.xml_file)

multilog/devices/process_condition_logger.py

@@ -2,6 +2,7 @@
 import datetime
 import logging
 import subprocess
+import yaml
 
 
 logger = logging.getLogger(__name__)
@@ -72,6 +73,62 @@ 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)
+
+    def write_nomad_files(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:
+            nomad_template = yaml.safe_load(f)
+        definitions = nomad_template.pop("definitions")
+        data = nomad_template.pop("data")
+        sensor_schema_template = nomad_template.pop("sensor_schema_template")
+        data.update(
+            {
+                "data_file": self.filename.split("/")[-1],
+            }
+        )
+        for sensor_name in self.meas_data:
+            sensor_name_nomad = sensor_name.replace(" ", "_").replace("-", "_")
+            data.update(
+                {
+                    sensor_name_nomad: {
+                        # "model": "your_field_here",
+                        "name": sensor_name_nomad,
+                        # "sensor_id": sensor_name.split(" ")[0],
+                        # "attached_to": sensor_name, # TODO this information is important!
+                        # "measured_property": ,
+                        # "type": sensor_type,
+                        # "notes": "TE_1_K air 155 mm over crucible",
+                        # "unit": self.unit[sensor_name],  # TODO
+                        "value_timestamp_rel": "#/data/value_timestamp_rel",
+                        "value_timestamp_abs": "#/data/value_timestamp_abs",
+                    }
+                }
+            )
+            sensor_schema = deepcopy(sensor_schema_template)
+            sensor_schema["section"]["quantities"]["value_log"]["m_annotations"][
+                "tabular"
+            ]["name"] = sensor_name
+            definitions["sections"]["Sensors_list"]["sub_sections"].update(
+                {sensor_name_nomad: sensor_schema}
+            )
+            definitions["sections"]["Sensors_list"]["m_annotations"]["plot"].append(
+                {
+                    "label": f"{sensor_name_nomad} over time",
+                    "x": "value_timestamp_rel",
+                    "y": [f"{sensor_name_nomad}/value_log"],
+                }
+            )
+        nomad_dict = {
+            "definitions": definitions,
+            "data": data,
+        }
+        with open(f"{directory}/{self.name}.archive.yaml", "w", encoding="utf-8") as f:
+            yaml.safe_dump(nomad_dict, f, sort_keys=False)
 
     def sample(self):
         """This function just exists to fit into the sampling structure

multilog/devices/pyrometer_array_lumasense.py

@@ -1,7 +1,9 @@
+from copy import deepcopy
 import datetime
 import logging
 import numpy as np
 from serial import Serial, SerialException
+import yaml
 
 
 logger = logging.getLogger(__name__)
@@ -49,8 +51,11 @@ def __init__(self, config, name="PyrometerArrayLumasense"):
             self.meas_data.update({sensor: []})
             self.emissivities.update({sensor: config["sensors"][sensor]["emissivity"]})
             self.t90s.update({sensor: config["sensors"][sensor]["t90"]})
-            self.set_emissivity(head_number, config["sensors"][sensor]["emissivity"])
-            self.set_emissivity(head_number, config["sensors"][sensor]["t90"])
+            if type(self.serial) != SerialMock:
+                self.set_emissivity(
+                    head_number, config["sensors"][sensor]["emissivity"]
+                )
+                self.set_emissivity(head_number, config["sensors"][sensor]["t90"])
 
     def _get_ok(self):
         """Check if command was accepted."""
@@ -108,7 +113,7 @@ def sample(self):
                 sampling.update({sensor: np.nan})
         return sampling
 
-    def init_otput(self, directory="./"):
+    def init_output(self, directory="./"):
         """Initialize the csv output file.
 
         Args:
@@ -125,6 +130,64 @@ def init_otput(self, directory="./"):
         with open(self.filename, "w", encoding="utf-8") as f:
             f.write(units)
             f.write(header)
+        self.write_nomad_files(directory)
+
+    def write_nomad_files(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:
+            nomad_template = yaml.safe_load(f)
+        definitions = nomad_template.pop("definitions")
+        data = nomad_template.pop("data")
+        sensor_schema_template = nomad_template.pop("sensor_schema_template")
+        data.update(
+            {
+                "data_file": self.filename.split("/")[-1],
+            }
+        )
+        for sensor_name in self.meas_data:
+            sensor_name_nomad = sensor_name.replace(" ", "_").replace("-", "_")
+            data.update(
+                {
+                    sensor_name_nomad: {
+                        # "model": "your_field_here",
+                        "name": sensor_name_nomad,
+                        # "sensor_id": sensor_name.split(" ")[0],
+                        # "attached_to": sensor_name, # TODO this information is important!
+                        # "measured_property": ,
+                        # "type": sensor_type,
+                        # "notes": "TE_1_K air 155 mm over crucible",
+                        # "unit": self.unit[sensor_name],  # TODO
+                        "emissivity": self.emissivities[sensor_name],
+                        "head_id": self.head_numbering[sensor_name],
+                        "value_timestamp_rel": "#/data/value_timestamp_rel",
+                        "value_timestamp_abs": "#/data/value_timestamp_abs",
+                    }
+                }
+            )
+            sensor_schema = deepcopy(sensor_schema_template)
+            sensor_schema["section"]["quantities"]["value_log"]["m_annotations"][
+                "tabular"
+            ]["name"] = sensor_name
+            definitions["sections"]["Sensors_list"]["sub_sections"].update(
+                {sensor_name_nomad: sensor_schema}
+            )
+            definitions["sections"]["Sensors_list"]["m_annotations"]["plot"].append(
+                {
+                    "label": f"{sensor_name_nomad} over time",
+                    "x": "value_timestamp_rel",
+                    "y": [f"{sensor_name_nomad}/value_log"],
+                }
+            )
+        nomad_dict = {
+            "definitions": definitions,
+            "data": data,
+        }
+        with open(f"{directory}/{self.name}.archive.yaml", "w", encoding="utf-8") as f:
+            yaml.safe_dump(nomad_dict, f, sort_keys=False)
 
     def save_measurement(self, time_abs, time_rel, sampling):
         """Write measurement data to file.