style: remove unused module, change style of string, fix codespell.

src/diffpy/confutils/__init__.py

@@ -13,9 +13,6 @@
 #
 ##############################################################################
 
-# some convenience imports
-from diffpy.confutils.config import ConfigBase
-
 # package version
 from diffpy.srxplanar.version import __version__
 

src/diffpy/confutils/tools.py

@@ -49,9 +49,9 @@ def _configPropertyRW(name):
     read and write
     """
     rv = property(
-        fget=lambda self: getattr(self.config, nm),
-        fset=lambda self, value: setattr(self.config, nm, value),
-        fdel=lambda self: delattr(self, nm),
+        fget=lambda self: getattr(self.config, name),
+        fset=lambda self, value: setattr(self.config, name, value),
+        fdel=lambda self: delattr(self, name),
         doc="attribute forwarded to self.config, read/write",
     )
     return rv
@@ -64,9 +64,9 @@ def str2bool(v):
 
 def opt2Str(opttype, optvalue):
     """Turn the value of one option to string, according to the option
-    type list of values are truned into "value1, value2, value3...".
+    type list of values are turned into "value1, value2, value3...".
 
-    :param opttype: string, type of opitons, for example 'str' or
+    :param opttype: string, type of options, for example 'str' or
         'intlist'
     :param optvalue: value of the option
     :return: string, usually stored in ConfigBase.config
@@ -105,15 +105,15 @@ def str2Opt(opttype, optvalue):
     """Convert the string to value of one option, according to the
     option type.
 
-    :param opttype: string, type of opitons, for example 'str' or
+    :param opttype: string, type of options, for example 'str' or
         'intlist'
     :param optvalue: string, value of the option
     :return: value of the option, usually stored in ConfigBase.config
     """
     # base converter
     conv = StrConv(opttype)
     if opttype.endswith("list"):
-        temp = re.split("\s*,\s*", optvalue)
+        temp = re.split(r"\s*,\s*", optvalue)
         rv = map(conv, temp) if len(temp) > 0 else []
     else:
         rv = conv(optvalue)
@@ -156,7 +156,7 @@ def checkCRC32(filename):
     """
     try:
         fd = open(filename, "rb")
-    except:
+    except Exception:
         return "Read error"
     eachLine = fd.readline()
     prev = 0
@@ -175,7 +175,7 @@ def checkMD5(filename, blocksize=65536):
     """
     try:
         fd = open(filename, "rb")
-    except:
+    except Exception:
         return "Read error"
     buf = fd.read(blocksize)
     md5 = hashlib.md5()

src/diffpy/srxplanar/__init__.py

@@ -14,11 +14,11 @@
 ##############################################################################
 
 # some convenience imports
-from diffpy.srxplanar.srxplanar import SrXplanar
-from diffpy.srxplanar.srxplanarconfig import SrXplanarConfig
+from diffpy.srxplanar.srxplanar import SrXplanar  # noqa: F401
+from diffpy.srxplanar.srxplanarconfig import SrXplanarConfig  # noqa: F401
 
 # package version
-from diffpy.srxplanar.version import __version__
+from diffpy.srxplanar.version import __version__  # noqa: F401
 
 # unit tests
 

src/diffpy/srxplanar/calculate.py

@@ -15,8 +15,6 @@
 
 import numpy as np
 import scipy.ndimage.filters as snf
-import scipy.ndimage.morphology as snm
-import scipy.sparse as ssp
 
 from diffpy.srxplanar.srxplanarconfig import _configPropertyR
 
@@ -53,7 +51,8 @@ class Calculate(object):
     extracrop = _configPropertyR("extracrop")
 
     def __init__(self, p):
-        # create parameter proxy, so that parameters can be accessed by self.parametername in read-only mode
+        # create parameter proxy, so that parameters can be
+        # accessed by self.parametername in read-only mode
         self.config = p
         self.prepareCalculation()
         return
@@ -106,26 +105,30 @@ def genIntegrationInds(self, mask=None):
         :return: self.bin_number
         """
         self.maskedmatrix = np.array(self.tthorqmatrix)
-        if mask == None:
+        if mask is None:
             # mask = np.zeros((self.ydimension, self.xdimension), dtype=bool)
             mask = np.zeros((len(self.yr), len(self.xr)), dtype=bool)
         ce = self.cropedges
         mask = mask[ce[2] : -ce[3], ce[0] : -ce[1]]
         self.maskedmatrix[mask] = 1000.0
 
         # extra crop
-        maskedmatrix = self.getMaskedmatrixPic()
-        # self.bin_number = np.array(np.histogram(maskedmatrix, self.bin_edges)[0], dtype=float)
+        self.getMaskedmatrixPic()
+        # self.bin_number = np.array(
+        #     np.histogram(maskedmatrix, self.bin_edges)[0],
+        #     dtype=float,
+        # )
         # self.bin_number[self.bin_number <= 0] = 1
         return  # self.bin_number
 
     def intensity(self, pic):
         """2D to 1D image integration, intensity of pixels are binned
         and then take average,
 
-        :param pic: 2D array, array of raw counts, corrections hould be
-            already applied :retrun: 2d array, [tthorq, intensity,
-            unceratinty] or [tthorq, intensity]
+        :param pic: 2D array, array of raw counts, corrections should be
+            already applied
+        :return: 2d array, [tthorq, intensity, unceratinty] or [tthorq,
+            intensity]
         """
 
         intensity = self.calculateIntensity(pic)
@@ -159,7 +162,7 @@ def getMaskedmatrixPic(self, pic=None):
             )
             self.bin_number[self.bin_number <= 0] = 1
 
-        if pic != None:
+        if pic is not None:
             ps = [max(s1, s2) for s1, s2 in zip(ce, ec)]
             rv = (
                 self.maskedmatrix[s[2] : s[3], s[0] : s[1]],
@@ -171,7 +174,8 @@ def calculateIntensity(self, pic):
         """Calculate the 1D intensity.
 
         :param pic: 2D array, array of raw counts, raw counts should be
-            corrected :retrun: 1d array, 1D integrated intensity
+            corrected
+        :return: 1d array, 1D integrated intensity
         """
 
         maskedmatrix, pic = self.getMaskedmatrixPic(pic)
@@ -182,9 +186,9 @@ def calculateIntensity(self, pic):
     def calculateVariance(self, pic):
         """Calculate the 1D intensity.
 
-        :param pic: 2D array, array of raw counts, corrections hould be
-            already applied :retrun: 1d array, variance of integrated
-            intensity
+        :param pic: 2D array, array of raw counts, corrections should be
+            already applied
+        :return: 1d array, variance of integrated intensity
         """
         maskedmatrix = self.getMaskedmatrixPic()
 
@@ -196,9 +200,9 @@ def calculateVariance(self, pic):
 
     def calculateVarianceLocal(self, pic):
         """Calculate the variance of raw counts of each pixel are
-        calculated according to their loacl variance.
+        calculated according to their local variance.
 
-        :param pic: 2d array, 2d image array, corrections hould be
+        :param pic: 2d array, 2d image array, corrections should be
             already applied
         :return: 2d array, variance of each pixel
         """
@@ -251,7 +255,10 @@ def genTTHMatrix(self):
         sourceyr = self.distance * sint * sinr
         sourcezr = self.distance * cost
 
-        # tthmatrix1 = np.zeros((self.ydimension, self.xdimension), dtype=float)
+        # tthmatrix1 = np.zeros(
+        #     (self.ydimension, self.xdimension),
+        #     dtype=float,
+        # )
         tthmatrix1 = np.zeros((len(self.yr), len(self.xr)), dtype=float)
         tthmatrix1 += ((-self.xr + sourcexr) * sourcexr).reshape(
             1, len(self.xr)
@@ -277,7 +284,10 @@ def genQMatrix(self):
         sourceyr = self.distance * sint * sinr
         sourcezr = self.distance * cost
 
-        # tthmatrix1 = np.zeros((self.ydimension, self.xdimension), dtype=float)
+        # tthmatrix1 = np.zeros(
+        #     (self.ydimension, self.xdimension),
+        #     dtype=float,
+        # )
         tthmatrix1 = np.zeros((len(self.yr), len(self.xr)), dtype=float)
         tthmatrix1 += ((-self.xr + sourcexr) * sourcexr).reshape(
             1, len(self.xr)
@@ -322,7 +332,11 @@ def _polarizationCorrection(self):
         :return: 2d array, correction matrix to apply on the image
         """
         if self.polcorrectionenable:
-            # tthmatrix = self.tthorqmatrix if self.integrationspace == 'twotheta' else self.genTTHMatrix()
+            # tthmatrix = (
+            #     self.tthorqmatrix
+            #     if self.integrationspace == "twotheta"
+            #     else self.genTTHMatrix()
+            # )
             tthmatrix = self.tthmatrix
             azimuthmatrix = self.azimuthmatrix
             p = 0.5 * (1 + (np.cos(tthmatrix)) ** 2)

src/diffpy/srxplanar/loadimage.py

@@ -15,11 +15,9 @@
 
 import fnmatch
 import os
-import sys
 import time
 
 import numpy as np
-from tifffile import imsave as saveImage
 
 from diffpy.srxplanar.srxplanarconfig import _configPropertyR
 
@@ -30,7 +28,7 @@ def openImage(im):
         rv = fabio.openimage.openimage(im)
         return rv.data
 
-except:
+except ImportError:
     import tifffile
 
     def openImage(im):
@@ -88,7 +86,7 @@ def loadImage(self, filename):
                     else:
                         image = openImage(filenamefull)
                     i = 10
-                except:
+                except FileNotFoundError:
                     i = i + 1
                     time.sleep(0.5)
             image = self.flipImage(image)
@@ -149,13 +147,13 @@ def genFileSet(
             file
         :return: set of str, a list of filenames
         """
-        filenames = self.filenames if filenames == None else filenames
-        opendir = self.opendirectory if opendir == None else opendir
+        filenames = self.filenames if filenames is None else filenames
+        opendir = self.opendirectory if opendir is None else opendir
         includepattern = (
-            self.includepattern if includepattern == None else includepattern
+            self.includepattern if includepattern is None else includepattern
         )
         excludepattern = (
-            self.excludepattern if excludepattern == None else excludepattern
+            self.excludepattern if excludepattern is None else excludepattern
         )
         # filter the filenames according to include and exclude pattern
         filelist = os.listdir(opendir)