update general loader, Readme and examples

Author: derollins

AFMReader/general_loader.py

@@ -65,7 +65,7 @@ def load(self) -> tuple[npt.NDArray | str, float | None]:  # noqa: C901
             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)
+                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":

README.md

@@ -129,13 +129,15 @@ image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk
 ### .h5-jpk
 
 You can open `.h5-jpk` files using the `load_h5jpk` function. Just pass in the path
-to the file, the channel name you want to use and the frame number to access.
+to the file and the channel name you want to use.
 (If in doubt, use `height_trace` or `measuredHeight_trace`).
 
+Note: Since `.h5-jpk` stores timeseries AFM data a dictionary of timestamps for each frame is also returned.
+
 ```python
 from AFMReader.h5_jpk import load_h5jpk
 
-image, pixel_to_nanometre_scaling_factor = load_h5jpk(file_path="./my_jpk_file.jpk", channel="height_trace", frame = 0)
+frames, pixel_to_nanometre_scaling_factor, timestamp_dict = load_h5jpk(file_path="./my_jpk_file.jpk", channel="height_trace")
 ```
 
 ### .stp

examples/example_01.ipynb

@@ -188,6 +188,48 @@
     "plt.show()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# H5-JPK Files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import the load_jpk function from AFMReader\n",
+    "from AFMReader.h5_jpk import load_h5jpk"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the JPK file as an image and pixel to nm scaling factor\n",
+    "FILE = \"../tests/resources/sample_0.h5-jpk\"\n",
+    "frames, pixel_to_nm_scaling, timestamps = load_h5jpk(file_path=FILE, channel=\"height_trace\", flip_image=True)\n",
+    "logger.info(f\"Loaded {len(frames)} frames from {FILE}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot the image\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "plt.imshow(image, cmap=\"afmhot\")\n",
+    "plt.show()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},