chore: Remove unused method, test and package dependencies

Closes #1036

With the delegation of much I/O (Input/Output) functionality to @SylviaWhittle `AFMReader` (see #1031) we have removed
most of the methods to the `io.LoadScan()` class. One that slipped through was `_spm_pixel_to_nm_scaling()` and this
commit removes it along with its associated test.

Further the delegation of reading AFM files using `AFMReader` means `TopoStats` no longer has explicit dependencies on
the `igor2`, `pySPM` or `tifffile` packages and so these have been removed from the `dependencies` section of
`pyproject.toml`. These are dependencies of `AFMReader` and will still be installed in virtual environments.

pyproject.toml

@@ -38,13 +38,11 @@ dependencies = [
   "art",
   "AFMReader",
   "h5py",
-  "igor2",
   "keras",
   "matplotlib",
   "numpy",
   "numpyencoder",
   "pandas",
-  "pySPM",
   "pyyaml",
   "ruamel.yaml",
   "schema",
@@ -54,7 +52,6 @@ dependencies = [
   "skan~=0.11.0",
   "snoop",
   "tensorflow",
-  "tifffile",
   "topoly",
   "tqdm",
 ]

tests/test_io.py

@@ -5,12 +5,10 @@
 import logging
 from datetime import datetime
 from pathlib import Path
-from unittest.mock import patch
 
 import h5py
 import numpy as np
 import pandas as pd
-import pySPM
 import pytest
 
 from topostats.io import (
@@ -603,33 +601,6 @@ def test_load_scan_topostats(load_scan_topostats: LoadScans) -> None:
     assert grain_trace_data.keys() == {"above"}
 
 
-@patch("pySPM.SPM.SPM_image.pxs")
-@pytest.mark.parametrize(
-    ("unit", "x", "y", "expected_px2nm"),
-    [
-        pytest.param("mm", 0.01, 0.01, 10000, id="mm units; square"),
-        pytest.param("um", 1.5, 1.5, 1500, id="um units; square"),
-        pytest.param("nm", 50, 50, 50, id="nm units; square"),
-        pytest.param("pm", 233, 233, 0.233, id="pm units; square"),
-        pytest.param("pm", 1, 512, 0.001, id="pm units; rectangular (thin)"),
-        pytest.param("pm", 512, 1, 0.512, id="pm units; rectangular (tall)"),
-    ],
-)
-def test__spm_pixel_to_nm_scaling(
-    mock_pxs,
-    load_scan_spm: LoadScans,
-    spm_channel_data: pySPM.SPM.SPM_image,
-    unit: str,
-    x: int,
-    y: int,
-    expected_px2nm: float,
-) -> None:
-    """Test extraction of pixels to nanometer scaling."""
-    mock_pxs.return_value = [(x, unit), (y, unit)]  # issue is that pxs is a func that returns the data
-    result = load_scan_spm._spm_pixel_to_nm_scaling(spm_channel_data)
-    assert result == expected_px2nm
-
-
 @pytest.mark.parametrize(
     ("load_scan_object", "length", "image_shape", "image_sum", "filename", "pixel_to_nm_scaling"),
     [

topostats/io.py

@@ -18,7 +18,6 @@
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
-import pySPM
 from AFMReader import asd, gwy, ibw, jpk, spm, topostats
 from numpyencoder import NumpyEncoder
 from ruamel.yaml import YAML, YAMLError
@@ -642,38 +641,6 @@ def load_spm(self) -> tuple[npt.NDArray, float]:
             LOGGER.error(f"File Not Found : {self.img_path}")
             raise
 
-    def _spm_pixel_to_nm_scaling(self, channel_data: pySPM.SPM.SPM_image) -> float:
-        """
-        Extract pixel to nm scaling from the SPM image metadata.
-
-        Parameters
-        ----------
-        channel_data : pySPM.SPM.SPM_image
-            Channel data from PySPM.
-
-        Returns
-        -------
-        float
-            Pixel to nm scaling factor.
-        """
-        unit_dict = {
-            "pm": 1e-3,
-            "nm": 1,
-            "um": 1e3,
-            "mm": 1e6,
-        }
-        px_to_real = channel_data.pxs()
-        # Has potential for non-square pixels but not yet implemented
-        pixel_to_nm_scaling = (
-            px_to_real[0][0] * unit_dict[px_to_real[0][1]],
-            px_to_real[1][0] * unit_dict[px_to_real[1][1]],
-        )[0]
-        if px_to_real[0][0] == 0 and px_to_real[1][0] == 0:
-            pixel_to_nm_scaling = 1
-            LOGGER.warning(f"[{self.filename}] : Pixel size not found in metadata, defaulting to 1nm")
-        LOGGER.debug(f"[{self.filename}] : Pixel to nm scaling : {pixel_to_nm_scaling}")
-        return pixel_to_nm_scaling
-
     def load_topostats(self) -> tuple[npt.NDArray, float]:
         """
         Load a .topostats file (hdf5 format).