Fix numpy 2.0 deprecation errors

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
@@ -21,16 +21,16 @@ repos:
     hooks:
       - id: nbcheckorder
   - repo: https://github.com/myint/docformatter
-    rev: v1.7.2
+    rev: v1.7.5
     hooks:
       - id: docformatter
   - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v2.0.2
+    rev: v2.0.4
     hooks:
       - id: autopep8
         args: ['--in-place', '--ignore=E501,W504']
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.272'
+    rev: 'v0.4.9'
     hooks:
       - id: ruff
         args: [--fix]

pyproject.toml

@@ -121,52 +121,22 @@ publishing = [
 "instamatic.autoconfig" = "instamatic.config.autoconfig:main"
 
 [tool.ruff]
+target-version = 'py37'
+line-length = 96
+
+[tool.ruff.lint]
 # Enable Pyflakes `E` and `F` codes by default.
 select = [
 	'F',  # Pyflakes
 	'E',  # pycodestyle (error)
 	'W',    # pycodestyle (warning)
-	# 'C90',  # mccabe
 	'I',    # isort
-	# 'N',    # pep8-naming
-	# 'D',    # pydocstyle
 	'UP',   # pyupgrade
-	# 'YTT',  # flake8-2020
-	# 'ANN',  # flake8-annotations
-	# 'S',    # flake8-bandit
-	'BLE',  # flake8-blind-except
-	# 'FBT',  # flake8-boolean-trap
-	# 'B',    # flake8-bugbear
 	'A',    # flake8-builtins
 	'COM',  # flake8-commas
 	'C4',   # flake8-comprehensions
-	# 'DTZ',  # flake8-datetimez
-	# 'T10',  # flake8-debugger
-	# 'EM',   # flake8-errmsg
-	# 'EXE',  # flake8-executable
-	# 'ISC',  # flake8-implicit-str-concat
-	# 'ICN',  # flake8-import-conventions
-	# 'G',    # flake8-logging-format
-	# 'INP',  # flake8-no-pep420
-	# 'PIE',  # flake8-pie
-	# 'T20',  # flake8-print
-	# 'PT',   # flake8-pytest-style
-	# 'Q',    # flake8-quotes
-	# 'RET',  # flake8-return
-	# 'SIM',  # flake8-simplify
 	'TID',  # flake8-tidy-imports
-	# 'TCH',  # flake8-type-checking
-	# 'ARG',  # flake8-unused-arguments
-	# 'PTH',  # flake8-use-pathlib
-	# 'ERA',  # eradicate
-	# 'PD',   # pandas-vet
-	# 'PGH',  # pygrep-hooks
-	# 'PL',   # Pylint
-	# 'PLC',  # Convention
-	# 'PLE',  # Error
-	# 'PLR',  # Refactor
-	# 'PLW',  # Warning
-	# 'TRY',  # tryceratops
+    'NPY201',  # numpy deprecation
 ]
 ignore = [
     'F401',
@@ -211,13 +181,5 @@ per-file-ignores = {}
 # Allow unused variables when underscore-prefixed.
 dummy-variable-rgx = '^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$'
 
-target-version = 'py37'
-line-length = 96
-
-
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ['instamatic']
-
-[tool.isort]
-profile = 'black'
-# force-single-line = true

scripts/center_images_smv.py

@@ -4,8 +4,7 @@
 import numpy as np
 from scipy import ndimage as ndi
 
-from instamatic.formats import read_adsc
-from instamatic.formats import write_adsc
+from instamatic.formats import read_adsc, write_adsc
 
 # Script to center the beam
 #

scripts/diagnose_beam_drift.py

@@ -7,16 +7,15 @@
 from tqdm.auto import tqdm
 
 from instamatic.formats import adscimage
-from instamatic.tools import find_beam_center
-from instamatic.tools import find_subranges
+from instamatic.tools import find_beam_center, find_subranges
 
 
 def insert_nan(arr, interval=10):
     repeat = interval - 1
     new = []
     for i, row in enumerate(arr):
         if not (i) % repeat:
-            new.append(np.array([np.NaN, np.NaN]))
+            new.append(np.array([np.nan, np.nan]))
         new.append(row)
     return np.array(new)
 
@@ -64,7 +63,7 @@ def get_drifts_per_scan_range(xy):
         drifts.append(distance)
 
         normalized_xy.append(sub_xy - o)
-        normalized_xy.append([np.NaN, np.NaN])
+        normalized_xy.append([np.nan, np.nan])
 
     normalized_xy = np.vstack(normalized_xy)
     drifts = np.array(drifts)
@@ -110,7 +109,7 @@ def get_drifts_per_scan_range(xy):
         xy = insert_nan(xy, interval=10)
 
     i = np.sum(xy, axis=1) == 0
-    xy[i] = np.NaN
+    xy[i] = np.nan
 
     print()
     print('                   mean            std dev             diff        ')

scripts/make_serialed_movie.py

@@ -21,7 +21,7 @@ def get_files(file_pat: str) -> list:
             df, d = read_ycsv(file_pat)
             fns = df.index.tolist()
         else:
-            f = open(file_pat, 'r')
+            f = open(file_pat)
             fns = [line.split('#')[0].strip() for line in f if not line.startswith('#')]
     else:
         fns = glob.glob(file_pat)

scripts/process_dm.py

@@ -2,8 +2,8 @@
 from pathlib import Path
 
 import numpy as np
-from skimage.exposure import rescale_intensity
 from PIL import Image
+from skimage.exposure import rescale_intensity
 
 from instamatic.processing.ImgConversionDM import ImgConversionDM as ImgConversion
 
@@ -45,14 +45,14 @@ def img_convert(credlog, tiff_path='tiff2', mrc_path='RED', smv_path='SMV'):
 
     n = len(image_fns)
     if n == 0:
-        print(f'No files found matching `tiff/*.tif`')
+        print('No files found matching `tiff/*.tif`')
         exit()
     else:
         print(n)
 
     buffer = []
 
-    with open(credlog, 'r') as f:
+    with open(credlog) as f:
         for line in f:
             if line.startswith('Data Collection Time'):
                 timestamp = line.split(':', 1)[-1].strip()

scripts/process_tpx.py

@@ -77,7 +77,7 @@ def reprocess(credlog, tiff_path=None, mrc_path=None, smv_path='SMV_reprocessed'
 
     n = len(image_fns)
     if n == 0:
-        print(f'No files found matching `tiff/*.tiff`')
+        print('No files found matching `tiff/*.tiff`')
         exit()
     else:
         print(n)
@@ -89,7 +89,7 @@ def reprocess(credlog, tiff_path=None, mrc_path=None, smv_path='SMV_reprocessed'
 
     # osc_angle = 0.53
 
-    with open(credlog, 'r') as f:
+    with open(credlog) as f:
         for line in f:
             if line.startswith('Camera length'):
                 camera_length = float(line.split()[2])

scripts/process_tvips.py

@@ -19,8 +19,7 @@
 import tifffile
 
 from instamatic.processing.ImgConversionTVIPS import ImgConversionTVIPS as ImgConversion
-from instamatic.tools import get_acquisition_time
-from instamatic.tools import relativistic_wavelength
+from instamatic.tools import get_acquisition_time, relativistic_wavelength
 
 
 def extract_image_number(s):
@@ -59,7 +58,7 @@ def img_convert(credlog, tiff_path=None, pets_path='PETS', mrc_path='RED', smv_p
     acquisition_time = res.acquisition_time
     overhead = res.overhead
 
-    with open(credlog, 'r') as f:
+    with open(credlog) as f:
         for line in f:
             if line.startswith('Data Collection Time'):
                 timestamp = line.split(':', 1)[-1].strip()

src/instamatic/camera/merlin_io.py

@@ -106,7 +106,7 @@ def load_mib(buffer: bytes, skip: int = 0):
     props = MIBProperties.from_buffer(buffer)
 
     merlin_frame_dtype = np.dtype([
-        ('header', np.string_, props.headsize),
+        ('header', np.bytes_, props.headsize),
         ('data', props.pixeltype, props.merlin_size),
     ])
 

src/instamatic/config/utils.py

@@ -43,7 +43,6 @@ def array_representer(dumper, data):
 ]:
     representer.add_representer(np_type, representer.represent_int)
 for np_type in [
-    np.float_,
     np.float16,
     np.float32,
     np.float64,

src/instamatic/formats/mrc.py

@@ -306,7 +306,7 @@ def is_readable(filename, no_strict_mrc=False):
         else:
             _logger.debug('Failed to read proper machine stamp - not MRC!')
             # return False
-    if not numpy.alltrue([h[v][0] > 0 for v in ('nx', 'ny', 'nz')]):
+    if not numpy.all([h[v][0] > 0 for v in ('nx', 'ny', 'nz')]):
         _logger.debug('Failed to read proper dimensions - not MRC!')
         return False
     return True
@@ -549,7 +549,7 @@ def read_image(filename, index=None, cache=None, no_strict_mrc=False, force_volu
             out = out.byteswap()
     finally:
         util.close(filename, f)
-    # assert(numpy.alltrue(numpy.logical_not(numpy.isnan(out))))
+    # assert(numpy.all(numpy.logical_not(numpy.isnan(out))))
     # if header_image_dtype.newbyteorder()==h.dtype:out = out.byteswap()
     return out, header
 
@@ -638,7 +638,7 @@ def write_image(filename, img, index=None, header=None, inplace=False):
     try:
         img = img.astype(mrc2numpy[numpy2mrc[img.dtype.type]])
     except BaseException:
-        raise TypeError('Unsupported type for MRC writing: %s' % str(img.dtype))
+        raise TypeError(f'Unsupported type for MRC writing: {img.dtype}')
 
     mode = 'rb+' if index is not None and (index > 0 or inplace and index > -1) else 'wb+'
     f = util.uopen(filename, mode)

src/instamatic/formats/xdscbf.py

@@ -95,13 +95,13 @@ def write(fname, data, header={}):
                     b'Content-Type: application/octet-stream;',
                     b'     conversions="x-CBF_BYTE_OFFSET"',
                     b'Content-Transfer-Encoding: BINARY',
-                    np.string_('X-Binary-Size: %d' % (len(binary_blob))),
+                    np.bytes_(f'X-Binary-Size: {len(binary_blob)}'),
                     b'X-Binary-ID: 1',
-                    np.string_('X-Binary-Element-Type: "%s"' % (dtype)),
+                    np.bytes_(f'X-Binary-Element-Type: "{dtype}"'),
                     b'X-Binary-Element-Byte-Order: LITTLE_ENDIAN',
-                    np.string_('X-Binary-Number-of-Elements: %d' % (dim1 * dim2)),
-                    np.string_('X-Binary-Size-Fastest-Dimension: %d' % dim1),
-                    np.string_('X-Binary-Size-Second-Dimension: %d' % dim2),
+                    np.bytes_(f'X-Binary-Number-of-Elements: {dim1 * dim2}'),
+                    np.bytes_(f'X-Binary-Size-Fastest-Dimension: {dim1}'),
+                    np.bytes_(f'X-Binary-Size-Second-Dimension: {dim2}'),
                     b'X-Binary-Size-Padding: 1',
                     b'',
                     STARTER + binary_blob,

src/instamatic/processing/ImgConversion.py

@@ -602,7 +602,7 @@ def write_beam_centers(self, path: str) -> None:
         for i, h in self.headers.items():
             centers[i - 1] = h['beam_center']
         for i in self.missing_range:
-            centers[i - 1] = [np.NaN, np.NaN]
+            centers[i - 1] = [np.nan, np.nan]
 
         np.savetxt(path / 'beam_centers.txt', centers, fmt='%10.4f')