Fix read tem data

operators/docker-bake.hcl

@@ -156,7 +156,7 @@ target "electron-count" {
 }
 
 target "electron-count-save" {
-  inherits = ["common", "operator-context", "output"]
+  inherits = ["common", "distiller-streaming-context", "output"]
   context = "operators/electron-count-save"
   dockerfile = "Containerfile"
   tags = ["${REGISTRY}/electron-count-save"]

operators/electron-count-save/Containerfile

@@ -1,4 +1,4 @@
-FROM interactem-operator
+FROM distiller-streaming
 
 RUN poetry add stempy h5py
 

operators/read-tem-data/operator.json

@@ -29,6 +29,14 @@
       "required": true
     }
   ],
+  "triggers": [
+    {
+      "name": "read_now",
+      "label": "Read data now",
+      "description": "Manually read and emit the data without waiting.",
+      "mode": "single"
+    }
+  ],
   "parallel_config": {
     "type": "none"
   }

operators/read-tem-data/run.py

@@ -1,9 +1,7 @@
-import time
 from pathlib import Path
 from typing import Any
 
 import ncempy
-import numpy as np
 
 from interactem.core.logger import get_logger
 from interactem.core.models.messages import BytesMessage, MessageHeader, MessageSubject
@@ -15,36 +13,40 @@
 data_dir = Path(f"{DATA_DIRECTORY}/raw_data_dir")
 
 @operator
-def read_data_pae(
-    inputs: BytesMessage | None, parameters: dict[str, Any]
+def read_data_ncempy(
+    inputs: BytesMessage | None, parameters: dict[str, Any], trigger=None
 ) -> BytesMessage | None:
-    """This reads data from disk and sends it on."""
-
-    # This operator does not require inputs
+    """Read and emit TEM data from a specified file when triggered."""
+    if trigger is None:
+        return None
 
     # Extract parameters
-    directory = parameters.get("directory", "/test_data")
+    directory = parameters.get("raw_data_dir", "/test_data")
     file = parameters.get("file", "test.emd")
-    # mount_dir = parameters.get("mount_dir", "~")
 
-    # TODO: Implement operator logic here
+    # Read data from disk
     logger.info("read_tem_data operator running...")
 
-    logger.info(f'directory: {directory}')
-    logger.info(f'mount directory: {data_dir}')
-    logger.info(f'file: {file}')
-    # file_path = Path(directory) / Path(file)
+    logger.info(f"parameter directory: {directory}")
+    logger.info(f"internal mount directory: {data_dir}")
+    logger.info(f"file name: {file}")
+
     file_path = data_dir / Path(file)
     try:
         dd = ncempy.read(file_path)
         data = dd['data']
         logger.info(f'file data shape: {data.shape}')
-    except Exception:
-        data = np.zeros((100, 100), dtype=np.uint8)
-        logger.info('Problem loading file. Using zeros array.')
-    time.sleep(3.0)
+    except Exception as e:
+        logger.info(f"Problem loading file. Error: {e}")
+        return None
 
-    # TODO: Process and return result
+    # Process and return result if the data was loaded successfully
     data_bytes = data.tobytes()
-    header = MessageHeader(subject=MessageSubject.BYTES, meta={'shape': data.shape, 'dtype': str(data.dtype)})
+    header = MessageHeader(
+        subject=MessageSubject.BYTES,
+        meta={
+            "shape": data.shape,
+            "dtype": str(data.dtype),
+        },
+    )
     return BytesMessage(header=header, data=data_bytes)