Respond to review from Neil

Author: derollins

AFMReader/general_loader.py

@@ -45,7 +45,7 @@ def load(self) -> tuple[npt.NDArray | str, float | None]:  # noqa: C901
         Returns
         -------
         tuple
-            The image data (stack if ''.asd'') and the pixel to nanometre scaling ratio.
+            The image data (stack if ''.asd'' or ''.h5-jpk'') and the pixel to nanometre scaling ratio.
 
         Raises
         ------

AFMReader/h5_jpk.py

@@ -46,7 +46,7 @@ def _parse_channel_name(channel: str) -> tuple[str, str]:
     return channel_type, trace_type
 
 
-def _get_channel_info(f: h5py.File, channel: str):
+def _get_channel_info(h5py_file: h5py.File, channel: str):
     """
     Retrieve channel-related HDF5 groups and dataset name.
 
@@ -69,13 +69,13 @@ def _get_channel_info(f: h5py.File, channel: str):
     """
     _parse_channel_name(channel)  # just for validation
 
-    channel_map = _discover_available_channels(f)
+    channel_map = _available_channels(h5py_file)
     if channel not in channel_map:
         raise ValueError(f"'{channel}' not found. Available channels: {list(channel_map)}")
 
     channel_path = channel_map[channel]
-    channel_group = f[channel_path]
-    measurement_group = f[channel_path.split("/")[0]]
+    channel_group = h5py_file[channel_path]
+    measurement_group = h5py_file[channel_path.split("/")[0]]
     dataset_name = channel.split("_")[0].capitalize()
 
     return channel_group, measurement_group, dataset_name
@@ -179,7 +179,7 @@ def _attr_to_bool(attr: bytes | str | bool | int | float) -> bool:
     return bool(attr)
 
 
-def _discover_available_channels(f: h5py.File) -> dict[str, str]:
+def _available_channels(f: h5py.File) -> dict[str, str]:
     """
     Discover all available scan channels in the HDF5 file.
 
@@ -263,8 +263,7 @@ def generate_timestamps(num_frames: int, line_rate: float, image_size: int) -> d
     dict
         A dictionary mapping frame labels (e.g., "frame 0") to timestamps in seconds.
     """
-    frame_interval = image_size / line_rate  # seconds per frame (height lines / lines per second)
-    timestamps = np.arange(num_frames) * frame_interval
+    timestamps = np.arange(num_frames) * (image_size / line_rate)
     # Compose a dictionary of timestamsps
     return {f"frame {i}": timestamp for i, timestamp in enumerate(timestamps)}
 

tests/test_h5jpk.py

@@ -33,7 +33,84 @@
             dict,
             48525583.047271535,
             id="test image 0",
-        )
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "height_retrace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            48517762.77380567,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "error_trace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            -360.7100517131785,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "error_retrace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            367.81162274907103,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "phase_retrace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            1741828.7412469066,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "phase_trace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            1734511.5577225098,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "amplitude_retrace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            275567.73614739266,
+            id="test image 0",
+        ),
+        pytest.param(
+            "sample_0.h5-jpk",
+            "amplitude_trace",
+            True,
+            1.171875,
+            (4, 128, 128),
+            float,
+            dict,
+            276296.25732934737,
+            id="test image 0",
+        ),
     ],
 )
 def test_load_h5jpk(