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style: Fix E731, E712, E501, F821, F401 flake8 issue in srxplanarconfig and trifffile.py #17

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Merged
merged 1 commit into from
Oct 20, 2025
Merged

style: Fix E731, E712, E501, F821, F401 flake8 issue in srxplanarconfig and trifffile.py #17

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87 changes: 57 additions & 30 deletions src/diffpy/srxplanar/srxplanarconfig.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,24 +13,14 @@
#
##############################################################################

import argparse
import os
import re
import sys
from configparser import ConfigParser
from functools import partial

import numpy as np

from diffpy.confutils.config import ConfigBase
from diffpy.confutils.tools import (
_configPropertyR,
_configPropertyRad,
_configPropertyRW,
)
from diffpy.confutils.tools import _configPropertyRad

_description = """
SrXplanar -- integrate 2D powder diffraction image to 1D with unceratinty propagation
SrXplanar -- integrate 2D powder diffraction image to 1D
with unceratinty propagation
"""
# Text to display after the argument help
_epilog = """
Expand All @@ -56,7 +46,10 @@
"config": "n",
"header": "n",
"f": "filename",
"h": "filename or list of filenames or filename pattern or list of filename pattern",
"h": (
"filename or list of filenames or filename pattern"
" or list of filename pattern"
),
"n": "*",
"d": [],
},
Expand Down Expand Up @@ -85,7 +78,7 @@
"d": False,
},
],
# Expeiment gropu
# Experiment group
[
"opendirectory",
{
Expand Down Expand Up @@ -113,7 +106,10 @@
{
"sec": "Experiment",
"s": "mask",
"h": "the mask file (support numpy .npy array, and tiff image, >0 stands for masked pixel)",
"h": (
"the mask file (support numpy .npy array, and tiff image,"
" >0 stands for masked pixel)"
),
"d": "",
"tt": "file",
},
Expand All @@ -124,7 +120,10 @@
"sec": "Control",
"config": "n",
"header": "n",
"h": "create a mask file according to current image file and value of addmask",
"h": (
"create a mask file according to"
" current image file and value of addmask"
),
"d": "",
},
],
Expand Down Expand Up @@ -237,7 +236,7 @@
"fliphorizontal",
{
"sec": "Beamline",
"h": "filp the image horizontally",
"h": "flip the image horizontally",
"n": "?",
"co": True,
"d": False,
Expand All @@ -247,7 +246,7 @@
"flipvertical",
{
"sec": "Beamline",
"h": "filp the image vertically",
"h": "flip the image vertically",
"n": "?",
"co": True,
"d": True,
Expand Down Expand Up @@ -356,7 +355,11 @@
"avgmask",
{
"sec": "Others",
"h": "create a dynamic averaging mask that mask pixel with too high or too low intensity compare to the pixels which have similar twotheta value",
"h": (
"create a dynamic averaging mask that mask pixel with"
" too high or too low intensity compare to the pixels"
" which have similar twotheta value"
),
"n": "?",
"co": True,
"d": True,
Expand Down Expand Up @@ -385,7 +388,10 @@
"cropedges",
{
"sec": "Others",
"h": "crop the image, maske pixels around the image edge (left, right, top, bottom), must larger than 0",
"h": (
"crop the image, maske pixels around the image edge"
" (left, right, top, bottom), must larger than 0"
),
"n": 4,
"tt": "array",
"t": "intlist",
Expand All @@ -399,9 +405,13 @@
"args": "n",
"config": "n",
"header": "n",
"h": "crop the edge pixels, first four means the number of pixels masked in each edge \
"h": (
"crop the edge pixels, first four means"
" the number of pixels masked in each edge \
(left, right, top, bottom), this crop is after all prepare calculation, \
so change this value does not require a config update, value must larger than 0",
so change this value does not require a config update,"
" value must larger than 0"
),
"n": 4,
"tt": "array",
"t": "intlist",
Expand All @@ -414,7 +424,10 @@
"sec": "Others",
"config": "n",
"header": "n",
"h": "set True to disable all calculation, will automaticly set True if createconfig or createmask",
"h": (
"set True to disable all calculation,"
" will automatically set True if createconfig or createmask"
),
"n": "?",
"co": True,
"d": False,
Expand Down Expand Up @@ -461,7 +474,11 @@
"args": "n",
"config": "n",
"header": "n",
"h": "a threshold for masked pixels in average masking, pixels with (self_int > avg_int * avgmaskhigh) will be masked",
"h": (
"a threshold for masked pixels in average masking,"
" pixels with (self_int > avg_int * avgmaskhigh)"
" will be masked"
),
"d": 2.0,
},
],
Expand All @@ -472,15 +489,18 @@
"args": "n",
"config": "n",
"header": "n",
"h": "a threshold for masked pixels in average masking, pixels with (self_int < avg_int * avgmasklow) will be masked",
"h": (
"a threshold for masked pixels in average masking,"
" pixels with (self_int < avg_int * avgmasklow) will be masked"
),
"d": 0.5,
},
],
]

_defaultdata = {
"configfile": ["srxplanar.cfg", "SrXplanar.cfg"],
"headertitle": "SrXplanar configration",
"headertitle": "SrXplanar configuration",
}


Expand Down Expand Up @@ -508,7 +528,12 @@ def _preInit(self, **kwargs):

for name in ["rotation", "tilt", "tthstep", "tthmax"]:
setattr(self.__class__, name, _configPropertyRad(name + "d"))
# cls._configlist['Experiment'].extend(['rotation', 'tilt', 'tthstep', 'tthmax'])
# cls._configlist['Experiment'].extend([
# 'rotation',
# 'tilt',
# 'tthstep',
# 'tthmax',
# ])
return

def _preUpdateSelf(self, **kwargs):
Expand Down Expand Up @@ -543,9 +568,11 @@ def _postUpdateConfig(self, **kwargs):
:param kwargs: optional kwargs
"""

if (self.createconfig != "") and (self.createconfig != None):
if (self.createconfig != "") and (self.createconfig is not None):
self.nocalculation = True
if (self.createconfigfull != "") and (self.createconfigfull != None):
if (self.createconfigfull != "") and (
self.createconfigfull is not None
):
self.nocalculation = True
if self.createmask != "":
self.nocalculation = True
Expand Down
38 changes: 20 additions & 18 deletions src/diffpy/srxplanar/tifffile.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -854,7 +854,7 @@ def series(self):
page.axes,
page.compression in TIFF_DECOMPESSORS,
)
if not shape in pages:
if shape not in pages:
shapes.append(shape)
pages[shape] = [page]
else:
Expand Down Expand Up @@ -954,8 +954,8 @@ def _omeseries(self):
):
continue
for value in annot:
for modul in value:
for along in modul:
for modulo in value:
for along in modulo:
if not along.tag[:-1].endswith("Along"):
continue
axis = along.tag[-1]
Expand Down Expand Up @@ -1215,14 +1215,14 @@ def _fromfile(self):
if tagcode > tag.code:
warnings.warn("tags are not ordered by code")
tagcode = tag.code
if not tag.name in tags:
if tag.name not in tags:
tags[tag.name] = tag
else:
# some files contain multiple IFD with same code
# e.g. MicroManager files contain two image_description
for ext in ("_1", "_2", "_3"):
name = tag.name + ext
if not name in tags:
if name not in tags:
tags[name] = tag
break

Expand Down Expand Up @@ -1292,7 +1292,7 @@ def _process_tags(self):
else:
self.sample_format = TIFF_SAMPLE_FORMATS[value[0]]

if not "photometric" in tags:
if "photometric" not in tags:
self.photometric = None

if "image_length" in tags:
Expand Down Expand Up @@ -1327,7 +1327,7 @@ def _process_tags(self):
warnings.warn(str(e))
self.imagej_tags = Record(adict)

if not "image_length" in self.tags or not "image_width" in self.tags:
if "image_length" not in self.tags or "image_width" not in self.tags:
# some GEL file pages are missing image data
self.image_length = 0
self.image_width = 0
Expand Down Expand Up @@ -1453,7 +1453,7 @@ def _process_tags(self):
self.shape = self._shape[2:4]
self.axes = "YX"

if not self.compression and not "strip_byte_counts" in tags:
if not self.compression and "strip_byte_counts" not in tags:
self.strip_byte_counts = numpy.prod(self.shape) * (
self.bits_per_sample // 8
)
Expand Down Expand Up @@ -1900,7 +1900,7 @@ def _fromfile(self, parent):
else:
value = struct.unpack(fmt, value[:size])

if not code in CUSTOM_TAGS:
if code not in CUSTOM_TAGS:
if len(value) == 1:
value = value[0]

Expand Down Expand Up @@ -1938,7 +1938,7 @@ class TiffSequence(object):
(2, 100, 256, 256)
"""

_axes_pattern = """
_axes_pattern = r"""
# matches Olympus OIF and Leica TIFF series
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
Expand Down Expand Up @@ -2115,12 +2115,12 @@ def __str__(self):
.rstrip()
)
for k, v in lists:
l = []
parse_list = []
for i, w in enumerate(v):
l.append(
parse_list.append(
"* %s[%i]\n %s" % (k, i, str(w).replace("\n", "\n "))
)
s.append("\n".join(l))
s.append("\n".join(parse_list))
return "\n".join(s)


Expand Down Expand Up @@ -2615,8 +2615,8 @@ def unpackints(data, dtype, itemsize, runlen=0):
dtypestr = ">" + dtype.char # dtype always big endian?

unpack = struct.unpack
l = runlen * (len(data) * 8 // (runlen * itemsize + skipbits))
result = numpy.empty((l,), dtype)
length = runlen * (len(data) * 8 // (runlen * itemsize + skipbits))
result = numpy.empty((length,), dtype)
bitcount = 0
for i in range(len(result)):
start = bitcount // 8
Expand Down Expand Up @@ -2760,7 +2760,7 @@ def natural_sorted(iterable):
def sortkey(x):
return [(int(c) if c.isdigit() else c) for c in re.split(numbers, x)]

numbers = re.compile("(\d+)")
numbers = re.compile(r"(\d+)")
return sorted(iterable, key=sortkey)


Expand Down Expand Up @@ -3421,7 +3421,7 @@ def __getitem__(self, key):
0x90000001: "name",
0x90000002: "power",
0x90000003: "wavelength",
0x90000004: "aquire",
0x90000004: "acquire",
0x90000005: "detchannel_name",
0x90000006: "power_bc1",
0x90000007: "power_bc2",
Expand Down Expand Up @@ -3850,7 +3850,9 @@ def main(argv=None):

import optparse

search_doc = lambda r, d: re.search(r, __doc__).group(1) if __doc__ else d
def search_doc(r, d):
return re.search(r, __doc__).group(1) if __doc__ else d

parser = optparse.OptionParser(
usage="usage: %prog [options] path",
description=search_doc("\n\n([^|]*?)\n\n", ""),
Expand Down