Merge pull request #11 from AFM-SPM/ns-rse/5-pre-commit

LICENSE.md → COPYING

@@ -658,7 +658,7 @@ notice like this when it starts in an interactive mode:
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
 
-The hypothetical commands `show w' and `show c' should show the appropriate
+The hypothetical commands `show w' and`show c' should show the appropriate
 parts of the General Public License.  Of course, your program's commands
 might be different; for a GUI interface, you would use an "about box".
 

README.md

@@ -4,14 +4,18 @@ A library for loading various AFM file formats.
 
 File format support: `.asd`
 
-## Usage:
+## Usage
 
 ## .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 want to use. (If in doubt use the `"TP"` topography channel).
+You can open `.asd` files using the `load_asd` function. Just pass in the path to the file and the channel name that you
+want to use. (If in doubt use the `"TP"` topography channel).
+
+Note: For `.asd` files, there seem to only ever be two channels in one file. `"TP"` (topography) is the main one you
+will want to use unless you know you specifically want something else.
 
-Note: For `.asd` files, there seem to only ever be two channels in one file. `"TP"` (topography) is the main one you will want to use unless you know you specifically want something else.
 Other channels: `"ER"` - Error, `"PH"` - Phase
+
 ```python
 from topofileformats import load_asd
 

examples/example_01.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,44 +11,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "file version: 0\n",
-      "{'channel1': 'TP', 'channel2': 'PH', 'header_length': 131, 'frame_header_length': 32, 'user_name_size': 14, 'comment_offset_size': 88, 'comment_size': 8, 'x_pixels': 256, 'y_pixels': 256, 'x_nm': 200, 'y_nm': 200, 'frame_time': 412.6285705566406, 'z_piezo_extension': 45.0, 'z_piezo_gain': 2.0, 'analogue_digital_range': '0x40000', 'analogue_digital_data_bits_size': 12, 'analogue_digital_resolution': 14, 'is_averaged': True, 'averaging_window': 1, 'year': 2022, 'month': 7, 'day': 15, 'hour': 16, 'minute': 44, 'second': 10, 'rounding_degree': 15, 'max_x_scan_range': 9900.0, 'max_y_scan_range': 4500.0, 'initial_frames': 142, 'num_frames': 142, 'afm_id': 0, 'file_id': 1110, 'user_name': 'biophys', 'scanner_sensitivity': 0.0, 'phase_sensitivity': 0.0, 'scan_direction': 10, 'comment_without_null': 'mica'}\n",
-      "Requested channel TP matches first channel in file: TP\n",
-      "Scaling factor: Type: TP -> TP | piezo extension 2.0 * piezo gain 45.0 = scaling factor 90.0\n",
-      "created voltage converter. ad_range: 0x40000 -> 262144, max voltage: 5.0, scaling factor: 90.0, resolution: 4096\n",
-      "Analogue to digital mapping | Range: 0x40000 -> (-5.0, 5.0)\n",
-      "Converter: <topofileformats.asd.BipolarConverter object at 0x104cbb5b0>\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "FILE = \"../tests/resources/sample_0.asd\"\n",
     "frames, pixel_to_nm_scaling, metadata = load_asd(file_path=FILE, channel=\"TP\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "image/png": 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IFwDAFMIFADCFcAEATCFcAABTCBcAwBTCBQAwhXABAEwhXAAAUwgXAMAUwgUAMIVwAQBMIVwAAFMIFwDAFMIFADCFcAEATCFcAABTOhSu4uJiTZgwQX379lVKSopmzZqlmpqaiDHnz59Xfn6++vXrpz59+mjOnDlqaGiIGFNXV6fp06erV69eSklJ0YoVK9Ta2nr9ZwMAuOl1KFwVFRXKz8/Xnj17VFpaqpaWFk2ZMkVNTU3hMcuWLdNbb72lLVu2qKKiQidOnNDs2bPDxy9evKjp06frwoULeu+99/TKK6+opKREq1at6ryzAgDctGKcc+5a7/z5558rJSVFFRUVmjhxooLBoPr3769Nmzbpxz/+sSTp008/1fDhw1VZWan77rtPb7/9tn74wx/qxIkTSk1NlSStX79eK1eu1Oeff66EhIQrft9QKCSfz6dJmqm4mPhrnT4AIEpaXYvKtU3BYFBer7dD972u97iCwaAkKSkpSZJUXV2tlpYWZWdnh8cMGzZMAwcOVGVlpSSpsrJSo0aNCkdLknJychQKhXTw4MF2v09zc7NCoVDEBgDonq45XG1tbVq6dKnuv/9+jRw5UpIUCASUkJCgxMTEiLGpqakKBALhMf8brUvHLx1rT3FxsXw+X3gbMGDAtU4bAGDcNYcrPz9fBw4c0KuvvtqZ82lXUVGRgsFgeDt27FiXf08AwLdT3LXcqaCgQNu3b9euXbt02223hff7/X5duHBBjY2NEc+6Ghoa5Pf7w2Pef//9iMe7dNXhpTFf5fF45PF4rmWqAICbTIeecTnnVFBQoK1bt2rnzp3KyMiIOD5u3DjFx8errKwsvK+mpkZ1dXXKysqSJGVlZenjjz/WyZMnw2NKS0vl9Xo1YsSI6zkXAEA30KFnXPn5+dq0aZO2bdumvn37ht+T8vl86tmzp3w+nxYuXKjCwkIlJSXJ6/XqiSeeUFZWlu677z5J0pQpUzRixAg9+uijWrt2rQKBgJ555hnl5+fzrAoAcEUduhw+Jiam3f0bNmzQggULJP33A8jLly/X5s2b1dzcrJycHL388ssRLwN+9tlnWrJkicrLy9W7d2/Nnz9fL7zwguLirq6jXA4PALZdz+Xw1/U5rmghXABgW9Q+xwUAwI1GuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgCuECAJhCuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgCuECAJhCuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgCuECAJhCuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgCuECAJhCuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgCuECAJjSoXAVFxdrwoQJ6tu3r1JSUjRr1izV1NREjJk0aZJiYmIitscffzxiTF1dnaZPn65evXopJSVFK1asUGtr6/WfDQDgphfXkcEVFRXKz8/XhAkT1NraqqefflpTpkzRoUOH1Lt37/C4RYsW6fnnnw/f7tWrV/jrixcvavr06fL7/XrvvfdUX1+vn/70p4qPj9evf/3rTjglAMDNrEPh2rFjR8TtkpISpaSkqLq6WhMnTgzv79Wrl/x+f7uP8Y9//EOHDh3SO++8o9TUVN1zzz365S9/qZUrV+q5555TQkLCNZwGAKC7uK73uILBoCQpKSkpYv/GjRuVnJyskSNHqqioSOfOnQsfq6ys1KhRo5Samhrel5OTo1AopIMHD7b7fZqbmxUKhSI2AED31KFnXP+rra1NS5cu1f3336+RI0eG9z/yyCMaNGiQ0tPTtX//fq1cuVI1NTV64403JEmBQCAiWpLCtwOBQLvfq7i4WGvWrLnWqQIAbiLXHK78/HwdOHBAu3fvjti/ePHi8NejRo1SWlqaJk+erCNHjmjIkCHX9L2KiopUWFgYvh0KhTRgwIBrmzgAwLRreqmwoKBA27dv17vvvqvbbrvtsmMzMzMlSbW1tZIkv9+vhoaGiDGXbn/T+2Iej0derzdiAwB0Tx0Kl3NOBQUF2rp1q3bu3KmMjIwr3mffvn2SpLS0NElSVlaWPv74Y508eTI8prS0VF6vVyNGjOjIdAAA3VCHXirMz8/Xpk2btG3bNvXt2zf8npTP51PPnj115MgRbdq0SdOmTVO/fv20f/9+LVu2TBMnTtTo0aMlSVOmTNGIESP06KOPau3atQoEAnrmmWeUn58vj8fT+WcIALipxDjn3FUPjolpd/+GDRu0YMECHTt2TD/5yU904MABNTU1acCAAXrooYf0zDPPRLy899lnn2nJkiUqLy9X7969NX/+fL3wwguKi7u6joZCIfl8Pk3STMXFxF/t9AEA3xKtrkXl2qZgMNjht386FK5vC8IFALZdT7iu+arCaLrU2la1SOayCwBoVYuk///f844wGa4zZ85Iknbr71GeCQDgepw5c0Y+n69D9zH5UmFbW5tqamo0YsQIHTt2jMvj23Hps26sT/tYn8tjfa6MNbq8K62Pc05nzpxRenq6YmM79sksk8+4YmNjdeutt0oSn+u6Atbn8lify2N9row1urzLrU9Hn2ldwr/HBQAwhXABAEwxGy6Px6PVq1fzoeVvwPpcHutzeazPlbFGl9eV62Py4gwAQPdl9hkXAKB7IlwAAFMIFwDAFMIFADDFZLjWrVun22+/XbfccosyMzP1/vvvR3tKUfHcc88pJiYmYhs2bFj4+Pnz55Wfn69+/fqpT58+mjNnztf+Ec+bza5duzRjxgylp6crJiZGb775ZsRx55xWrVqltLQ09ezZU9nZ2Tp8+HDEmNOnTysvL09er1eJiYlauHChzp49ewPPoutcaX0WLFjwtZ+p3NzciDE36/oUFxdrwoQJ6tu3r1JSUjRr1izV1NREjLma36m6ujpNnz5dvXr1UkpKilasWKHW1tYbeSpd5mrWaNKkSV/7GXr88ccjxlzvGpkL12uvvabCwkKtXr1aH374ocaMGaOcnJyIf5iyO7n77rtVX18f3nbv3h0+tmzZMr311lvasmWLKioqdOLECc2ePTuKs+16TU1NGjNmjNatW9fu8bVr1+rFF1/U+vXrVVVVpd69eysnJ0fnz58Pj8nLy9PBgwdVWlqq7du3a9euXVq8ePGNOoUudaX1kaTc3NyIn6nNmzdHHL9Z16eiokL5+fnas2ePSktL1dLSoilTpqipqSk85kq/UxcvXtT06dN14cIFvffee3rllVdUUlKiVatWReOUOt3VrJEkLVq0KOJnaO3ateFjnbJGzph7773X5efnh29fvHjRpaenu+Li4ijOKjpWr17txowZ0+6xxsZGFx8f77Zs2RLe98knnzhJrrKy8gbNMLokua1bt4Zvt7W1Ob/f737729+G9zU2NjqPx+M2b97snHPu0KFDTpL74IMPwmPefvttFxMT4/7zn//csLnfCF9dH+ecmz9/vps5c+Y33qc7rc/JkyedJFdRUeGcu7rfqb///e8uNjbWBQKB8Jg///nPzuv1uubm5ht7AjfAV9fIOee+973vuZ///OffeJ/OWCNTz7guXLig6upqZWdnh/fFxsYqOztblZWVUZxZ9Bw+fFjp6ekaPHiw8vLyVFdXJ0mqrq5WS0tLxFoNGzZMAwcO7LZrdfToUQUCgYg18fl8yszMDK9JZWWlEhMTNX78+PCY7OxsxcbGqqqq6obPORrKy8uVkpKioUOHasmSJTp16lT4WHdan2AwKElKSkqSdHW/U5WVlRo1apRSU1PDY3JychQKhXTw4MEbOPsb46trdMnGjRuVnJyskSNHqqioSOfOnQsf64w1MvVHdr/44gtdvHgx4oQlKTU1VZ9++mmUZhU9mZmZKikp0dChQ1VfX681a9bowQcf1IEDBxQIBJSQkKDExMSI+6SmpioQCERnwlF26bzb+/m5dCwQCCglJSXieFxcnJKSkrrFuuXm5mr27NnKyMjQkSNH9PTTT2vq1KmqrKxUjx49us36tLW1aenSpbr//vs1cuRISbqq36lAINDuz9elYzeT9tZIkh555BENGjRI6enp2r9/v1auXKmamhq98cYbkjpnjUyFC5GmTp0a/nr06NHKzMzUoEGD9Prrr6tnz55RnBmsmjt3bvjrUaNGafTo0RoyZIjKy8s1efLkKM7sxsrPz9eBAwci3jNGpG9ao/99v3PUqFFKS0vT5MmTdeTIEQ0ZMqRTvreplwqTk5PVo0ePr13F09DQIL/fH6VZfXskJibqrrvuUm1trfx+vy5cuKDGxsaIMd15rS6d9+V+fvx+/9cu9GltbdXp06e75boNHjxYycnJqq2tldQ91qegoEDbt2/Xu+++q9tuuy28/2p+p/x+f7s/X5eO3Sy+aY3ak5mZKUkRP0PXu0amwpWQkKBx48aprKwsvK+trU1lZWXKysqK4sy+Hc6ePasjR44oLS1N48aNU3x8fMRa1dTUqK6urtuuVUZGhvx+f8SahEIhVVVVhdckKytLjY2Nqq6uDo/ZuXOn2trawr+A3cnx48d16tQppaWlSbq518c5p4KCAm3dulU7d+5URkZGxPGr+Z3KysrSxx9/HBH30tJSeb1ejRgx4sacSBe60hq1Z9++fZIU8TN03Wt0jReTRM2rr77qPB6PKykpcYcOHXKLFy92iYmJEVeodBfLly935eXl7ujRo+5f//qXy87OdsnJye7kyZPOOecef/xxN3DgQLdz5063d+9el5WV5bKysqI866515swZ99FHH7mPPvrISXK///3v3UcffeQ+++wz55xzL7zwgktMTHTbtm1z+/fvdzNnznQZGRnuyy+/DD9Gbm6uGzt2rKuqqnK7d+92d955p5s3b160TqlTXW59zpw545588klXWVnpjh496t555x333e9+1915553u/Pnz4ce4WddnyZIlzufzufLycldfXx/ezp07Fx5zpd+p1tZWN3LkSDdlyhS3b98+t2PHDte/f39XVFQUjVPqdFdao9raWvf888+7vXv3uqNHj7pt27a5wYMHu4kTJ4YfozPWyFy4nHPupZdecgMHDnQJCQnu3nvvdXv27In2lKLi4YcfdmlpaS4hIcHdeuut7uGHH3a1tbXh419++aX72c9+5r7zne+4Xr16uYceesjV19dHccZd791333WSvrbNnz/fOfffS+KfffZZl5qa6jwej5s8ebKrqamJeIxTp065efPmuT59+jiv1+see+wxd+bMmSicTee73PqcO3fOTZkyxfXv39/Fx8e7QYMGuUWLFn3tfwpv1vVpb10kuQ0bNoTHXM3v1L///W83depU17NnT5ecnOyWL1/uWlpabvDZdI0rrVFdXZ2bOHGiS0pKch6Px91xxx1uxYoVLhgMRjzO9a4R/6wJAMAUU+9xAQBAuAAAphAuAIAphAsAYArhAgCYQrgAAKYQLgCAKYQLAGAK4QIAmEK4AACmEC4AgCmECwBgyv8BeuOo1mVX2gkAAAAASUVORK5CYII=",
-      "text/plain": [
-       "<Figure size 640x480 with 1 Axes>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "create_animation(file_name=\"sample_0\", frames=frames)"
    ]
@@ -71,8 +46,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.9"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

tests/test_asd.py

@@ -1,18 +1,15 @@
 """Test the functioning of loading .asd files."""
-
-from topofileformats.asd import load_asd
-
 from pathlib import Path
 import pytest
 
-import numpy as np
+from topofileformats.asd import load_asd
 
 BASE_DIR = Path.cwd()
 RESOURCES = BASE_DIR / "tests" / "resources"
 
 
 @pytest.mark.parametrize(
-    "file_name, channel, number_of_frames, pixel_to_nm_scaling",
+    ("file_name", "channel", "number_of_frames", "pixel_to_nm_scaling"),
     [
         # File type 0
         (
@@ -30,11 +27,8 @@
         ),
     ],
 )
-def test_load_asd(
-    file_name: str, channel: str, number_of_frames: int, pixel_to_nm_scaling: float
-) -> None:
+def test_load_asd(file_name: str, channel: str, number_of_frames: int, pixel_to_nm_scaling: float) -> None:
     """Test the normal operation of loading a .asd file."""
-
     result_frames = list
     result_pixel_to_nm_scaling = float
     result_metadata = dict

topofileformats/__init__.py

@@ -0,0 +1 @@
+"""topofileformats."""