Add file type: SPM

.pre-commit-config.yaml

@@ -32,13 +32,13 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.1
+    rev: v0.4.2
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.0
+    rev: 24.4.2
     hooks:
       - id: black
         types: [python]

README.md

@@ -19,16 +19,17 @@ for use with [TopoStats](https://github.com/AFM-SPM/TopoStats).
 
 Supported file formats
 
-| File format | Description    |
-|-------------|----------------|
-| `.asd`      | High-speed AFM |
+| File format | Description      |
+|-------------|------------------|
+| `.asd`      | High-speed AFM   |
+| `.spm`      | [Bruker's Format](https://www.bruker.com/)  |
+| `.jpk`      | [Bruker](https://www.bruker.com/) |
 
 Support for the following additional formats is planned. Some of these are already supported in TopoStats and are
 awaiting refactoring to move their functionality into topofileformats these are denoted in bold below.
 
 | File format | Description                                             | Status                                     |
 |-------------|---------------------------------------------------------|--------------------------------------------|
-| `.spm`      | [Bruker](https://www.bruker.com/)                       | TopoStats supported, to be migrated (#16). |
 | `.ibw`      | [WaveMetrics](https://www.wavemetrics.com/)             | TopoStats supported, to be migrated (#17). |
 | `.gwy`      | [Gwyddion](http://gwyddion.net/)                        | TopoStats supported, to be migrated (#1).  |
 | `.nhf`      | [Nanosurf](https://www.nanosurf.com/en/)                | To Be Implemented.                         |
@@ -40,6 +41,18 @@ awaiting refactoring to move their functionality into topofileformats these are
 If you wish to process AFM images supported by `topofileformats` it is recommend you use
 [TopoStats](https://github.com/AFM-SPM/TopoStats) to do so, however the library can be used on its own.
 
+### .spm
+
+You can open `.spm` files using the `load_spm` function. Just pass in the path to the file and the
+channel name that you want to use. (If in doubt use one of the following: "Height", "ZSensor",
+"Height Sensor").
+
+```python
+from topofileformats.spm import load_spm
+
+image, pixel_to_nanometre_scaling_factor = load_spm(file_path="./my_spm_file.spm", channel="Height")
+```
+
 ### .asd
 
 You can open `.asd` files using the `load_asd` function. Just pass in the path to the file and the channel name that you
@@ -51,9 +64,20 @@ will want to use unless you know you specifically want something else.
 Other channels: `"ER"` - Error, `"PH"` - Phase
 
 ```python
-from topofileformats import load_asd
+from topofileformats.asd import load_asd
+
+frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd", channel="TP")
+```
+
+### .jpk
+
+You can open `.jpk` files using the `load_jpk` function. Just pass in the path
+to the file and the channel name you want to use. (If in doubt, use `height_trace` or `measuredHeight_trace`).
+
+```python
+from topofileformats.jpk import load_jpk
 
-frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd")
+image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk", channel="height_trace")
 ```
 
 ## Contributing

examples/example_01.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# SPM Files"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -8,6 +15,52 @@
    "source": [
     "from pathlib import Path\n",
     "\n",
+    "# Import the load_spm from topofileformats\n",
+    "from topofileformats.spm import load_spm\n",
+    "from topofileformats.logging import logger\n",
+    "\n",
+    "logger.enable(__package__)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the SPM file as an image and pixel to nm scaling factor\n",
+    "FILE = \"../tests/resources/sample_0.spm\"\n",
+    "image, pixel_to_nm_scaling = load_spm(FILE, channel=\"Height\")\n",
+    "logger.info(f\"Loaded a {image.shape} image with a pixel to nm scaling factor of {pixel_to_nm_scaling} nm/pixel.\")"
+   ]
+  },
+  {
+   "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": {},
+   "source": [
+    "# ASD Files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import the load_asd from topofileformats\n",
     "from topofileformats.asd import load_asd, create_animation"
    ]
   },
@@ -17,8 +70,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "FILE = Path(\"../tests/resources/sample_0.asd\")\n",
-    "frames, pixel_to_nm_scaling, metadata = load_asd(file_path=FILE, channel=\"TP\")"
+    "# Load the ASD file as a list of frames, the pixel to nm scaling factor and the metadata\n",
+    "FILE = \"../tests/resources/sample_0.asd\"\n",
+    "frames, pixel_to_nm_scaling, metadata = load_asd(file_path=FILE, channel=\"TP\")\n",
+    "logger.info(f\"Loaded {len(frames)} frames from {FILE}\")"
    ]
   },
   {
@@ -27,7 +82,64 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "create_animation(file_name=\"sample_0\", frames=frames)"
+    "# Plot a frame\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "frame_number = 55\n",
+    "plt.imshow(frames[frame_number], cmap=\"afmhot\")\n",
+    "plt.title(f\"Frame {frame_number}\")\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create a gif of the frames using the create_animation function. This is slow for large files.\n",
+    "create_animation(file_name=\"sample_0\", frames=frames, file_format=\".gif\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# JPK Files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import the load_jpk function from topofileformats\n",
+    "from topofileformats.jpk import load_jpk"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the IBW file as an image and pixel to nm scaling factor\n",
+    "FILE = \"../tests/resources/sample_0.jpk\"\n",
+    "image, pixel_to_nm_scaling = load_jpk(file_path=FILE, channel=\"height_trac\")"
+   ]
+  },
+  {
+   "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()"
    ]
   }
  ],

pyproject.toml

@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 
 keywords = [
@@ -30,7 +31,9 @@ keywords = [
 
 dependencies = [
   "matplotlib",
-  "numpy",
+  "tifffile",
+  "pySPM",
+  "pySPM",
   "loguru",
 ]
 
@@ -134,3 +137,11 @@ convention = "numpy"
 
 [tool.ruff.flake8-pytest-style]
 fixture-parentheses = true
+
+[tool.coverage.run]
+source = ["topofileformats"]
+omit = [
+  "topofileformats/_version.py",
+  "*tests*",
+  "**/__init__*",
+]