Merge pull request #152 from derollins/derollins/h5jpk

Author: ns-rse

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
         types: [python, yaml, markdown]
 
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.18.1
+    rev: v0.18.0
     hooks:
       - id: markdownlint-cli2
         args: []

AFMReader/asd.py

@@ -2,34 +2,32 @@
 
 import errno
 import os
-from pathlib import Path
 import sys
+from pathlib import Path
 
-
+import matplotlib.pyplot as plt
 import numpy as np
 import numpy.typing as npt
-import matplotlib.pyplot as plt
 from matplotlib import animation
 
-
-from AFMReader.logging import logger
 from AFMReader.io import (
-    read_int32,
-    read_int16,
-    read_float,
+    read_ascii,
     read_bool,
+    read_double,
+    read_float,
     read_hex_u32,
-    read_ascii,
-    read_uint8,
-    read_null_separated_utf8,
     read_int8,
-    read_double,
+    read_int16,
+    read_int32,
+    read_null_separated_utf8,
+    read_uint8,
     skip_bytes,
 )
-
+from AFMReader.logging import logger
 
 if sys.version_info.minor < 11:
     from typing import Any, BinaryIO
+
     from typing_extensions import Self
 else:
     from typing import Any, BinaryIO, Self

AFMReader/general_loader.py

@@ -4,7 +4,7 @@
 
 import numpy.typing as npt
 
-from AFMReader import asd, gwy, ibw, jpk, spm, stp, top, topostats
+from AFMReader import asd, gwy, h5_jpk, ibw, jpk, spm, stp, top, topostats
 from AFMReader.logging import logger
 
 logger.enable(__package__)
@@ -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
         ------
@@ -64,6 +64,8 @@ def load(self) -> tuple[npt.NDArray | str, float | None]:  # noqa: C901
                 image, pixel_to_nanometre_scaling_factor = jpk.load_jpk(self.filepath, self.channel)
             elif self.suffix == ".spm":
                 image, pixel_to_nanometre_scaling_factor = spm.load_spm(self.filepath, self.channel)
+            elif self.suffix == ".h5-jpk":
+                image, pixel_to_nanometre_scaling_factor, _ = h5_jpk.load_h5jpk(self.filepath, self.channel)
             elif self.suffix == ".stp":
                 image, pixel_to_nanometre_scaling_factor = stp.load_stp(self.filepath)
             elif self.suffix == ".top":

AFMReader/gwy.py

@@ -1,13 +1,13 @@
 """For decoding and loading .gwy AFM file format into Python Numpy arrays."""
 
-from pathlib import Path
 import re
+from pathlib import Path
 from typing import Any, BinaryIO
 
-from loguru import logger
 import numpy as np
+from loguru import logger
 
-from AFMReader.io import read_uint32, read_null_terminated_string, read_char, read_double
+from AFMReader.io import read_char, read_double, read_null_terminated_string, read_uint32
 
 
 def load_gwy(file_path: Path | str, channel: str) -> tuple[np.ndarray[Any, np.float64], float]: