Apply pep8 conventions to files

imageprocessing/binaryPreparer.py

@@ -1,22 +1,11 @@
-import io, os, sys, errno
-from PIL import Image, ImageMath
-from array import array
 import numpy as np
 
-import struct
-
-import time
-
-from skimage.transform import resize
-from skimage.io import imsave
-from skimage.io import imshow
-
 import logging
 
 logger = logging.getLogger(__name__)
 
 
-def processBinary(path, sliceSize, sliceFrom = None, sliceTo = None, littleEndian = False):
+def processBinary(path, sliceSize, sliceFrom=None, sliceTo=None, littleEndian=False):
     logger.debug('littleEndian: ' + str(littleEndian))
 
     rawFile = open(path, 'rb')
@@ -44,14 +33,13 @@ def processBinary(path, sliceSize, sliceFrom = None, sliceTo = None, littleEndia
     '''
 
     if (sliceFrom is not None and
-        sliceTo is not None):
-        numberOfSlices = sliceTo - sliceFrom + 1;
-        rawFile.seek(sliceFrom * bytesPerSlice, 0);
+            sliceTo is not None):
+
+        numberOfSlices = sliceTo - sliceFrom + 1
+        rawFile.seek(sliceFrom * bytesPerSlice, 0)
 
     floats = np.empty((1, numberOfSlices * floatsPerSlice), dtype=np.float32)
 
-    floatsMin = None
-    floatsMax = None
     endianString = '>'
     if littleEndian is True:
         endianString = '<'

imageprocessing/sliceMapCreator.py

@@ -1,29 +1,21 @@
-import io, os, sys
-import errno
-from skimage import img_as_ubyte, img_as_float
-from skimage.io import Image, imsave, use_plugin, imshow
+import io
+from skimage import img_as_ubyte
 from skimage.transform import resize
 
-from PIL import Image
+from Pillow import Image
 
 from django.conf import settings
 
 from multiprocessing import Process, cpu_count, Queue
 
-from array import array
 import numpy as np
 import math
-import argparse
-import json
 import copy
 
 import logging
 
 logger = logging.getLogger(__name__)
 
-import pdb
-
-#use_plugin('freeimage')
 
 class Sprite(object):
     imagesAsArrays = None
@@ -40,6 +32,7 @@ class Sprite(object):
     numberOfSprites = 0
     slicesPerSprite = 0
 
+
 def __initializeSprite(imageFrom, imageTo, sliceShape, dtype):
 
     imagesPerRow, totalRows, imagesToProcess, numberOfSprites, slicesPerSprite, zDownScalingFactor = __calculateRowsAndColsOfSpriteMap(imageFrom, imageTo)
@@ -49,10 +42,9 @@ def __initializeSprite(imageFrom, imageTo, sliceShape, dtype):
     outputImageArrays = []
     for counter in range(0, numberOfSprites):
         outputImageArray = np.empty((sliceShape[0] * totalRows, sliceShape[1] * imagesPerRow), dtype=dtype)
-        outputImageArray.setflags(write = True)
+        outputImageArray.setflags(write=True)
         outputImageArrays.append(outputImageArray)
 
-
     sprite = Sprite()
     sprite.imagesToProcess = imagesToProcess
     sprite.imagesPerRow = imagesPerRow
@@ -63,12 +55,13 @@ def __initializeSprite(imageFrom, imageTo, sliceShape, dtype):
 
     return sprite
 
+
 def __calculateRowsAndColsOfSpriteMap(imageFrom, imageTo):
     imagesToProcess = imageTo - imageFrom + 1
     slicesPerSprite = imagesToProcess
 
     # upperbound are 25 ^ 2 slices per map
-    maxSlicesPerMap = settings.MAX_NUMBER_SLICES_PER_MAP;
+    maxSlicesPerMap = settings.MAX_NUMBER_SLICES_PER_MAP
 
     zDownScalingActivated = settings.Z_DOWNSCALING_ACTIVATED
     zDownScalingFactor = 1
@@ -80,7 +73,6 @@ def __calculateRowsAndColsOfSpriteMap(imageFrom, imageTo):
         numberOfSprites = 1
         zDownScalingFactor = int(math.ceil(imagesToProcess / maxSlicesPerMap))
 
-
     imagesToProcess = int(math.floor(imagesToProcess / float(zDownScalingFactor)))
 
     # stretch the whole number of images on to the sprites
@@ -99,6 +91,7 @@ def __calculateRowsAndColsOfSpriteMap(imageFrom, imageTo):
 
     return (imagesPerRow, totalRows, imagesToProcess, numberOfSprites, slicesPerSprite, zDownScalingFactor)
 
+
 def __copyImageToSprite(sliceImage, destArray, sprite):
     numY, numX = sliceImage.shape
 
@@ -109,6 +102,7 @@ def __copyImageToSprite(sliceImage, destArray, sprite):
 
     return destArray
 
+
 def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, destSize):
 
     if len(frames.shape) != 4:
@@ -117,10 +111,6 @@ def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, des
     sprites = []
     imagesPerRow, totalRows, imagesToProcess, numberOfSprites, slicesPerSprite, zDownScalingFactor = __calculateRowsAndColsOfSpriteMap(imageFrom, imageTo)
 
-    frameShapeLength = len(frames.shape)
-    indexX = frameShapeLength - 1
-    indexY = indexX - 1
-
     upperBoundPixels = 16384
 
     if frames.shape[3] * imagesPerRow > upperBoundPixels:
@@ -132,7 +122,7 @@ def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, des
         logger.debug('sliceMapCreator resizing slices to (%d, %d)' % newImageShape)
         for frameCounter in range(0, frames.shape[0]):
             imageCounter = 0
-            cpus=cpu_count()
+            cpus = cpu_count()
             imagesPerCpu = int(math.ceil(frames.shape[1] / float(cpus)))
             processes = []
             queues = [Queue() for i in range(0, cpus)]
@@ -153,7 +143,6 @@ def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, des
             for process in processes:
                 process.start()
 
-
             resultFrames = []
             logger.debug('sliceMapCreator empty queues')
             for queue in queues:
@@ -169,11 +158,9 @@ def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, des
                     newFrames[frameCounter][imageCounter] = image
                     imageCounter += 1
 
-
             for process in processes:
                 process.join()
 
-
             '''
             old sequential implementation
 
@@ -205,11 +192,12 @@ def processFrames(frames, frameFrom, frameTo, imageFrom, imageTo, imgFormat, des
 
     return __resizeSprites(sprites, destSize, imgFormat)
 
+
 def processFrame(frame, frameNumber, imageFrom, imageTo, zDownScalingFactor):
     logger.debug('sliceMapCreator frameNumber %d' % frameNumber)
 
     if len(frame) is 0:
-      raise ValueError('could not find any frame')
+        raise ValueError('could not find any frame')
 
     firstSlice = frame[0]
 
@@ -245,6 +233,7 @@ def processFrame(frame, frameNumber, imageFrom, imageTo, zDownScalingFactor):
 
     return sprite
 
+
 def generateInfo(sprites, frameFrom, frameTo, imageFrom, imageTo):
     logger.debug('sliceMapCreator generating and saving .js info file')
 
@@ -263,14 +252,13 @@ def generateInfo(sprites, frameFrom, frameTo, imageFrom, imageTo):
         infoObject['frameFrom'] = frameFrom
         infoObject['frameTo'] = frameTo
 
-
     return infoObject
 
+
 def __resizeSprites(sprites, destSize, imgFormat):
     returnSprites = {}
     exponentMin = 9
     exponent = exponentMin
-    destWidth = 0
 
     firstSprite = sprites[0]
     # hardcoded value, 2^12
@@ -293,7 +281,6 @@ def __resizeSprites(sprites, destSize, imgFormat):
         if pot > widthUpperBound:
             exponentFound = True
             exponent = exponent
-            destWidth = int(math.pow(2, exponent))
         else:
             exponent += 1
 
@@ -321,7 +308,7 @@ def __resizeSprites(sprites, destSize, imgFormat):
                     pilImage = pilImage.convert('RGBA')
                     try:
                         pilImage.save(buff, format='WEBP', quality=quality)
-                    except OSError as e:
+                    except OSError:
                         # due to a bug in the library of webp, the webp encoder fails for high file sizes
                         # --> if this is a big 'destSize', we have to try it again with lower quality levels
                         logger.debug('sliceMapCreator failed to store webp with size of %dpx and quality value of %d' % (destSize, quality))
@@ -338,13 +325,12 @@ def __resizeSprites(sprites, destSize, imgFormat):
                     pilImage.save(buff, format='JPEG', quality=quality, progressive=True)
                     contenttype += 'jpeg'
 
-
                 logger.debug('sliceMapCreator image with res %d has size of: %d' % (destSize, buff.tell()))
 
-                buff.seek(0,0)
+                buff.seek(0, 0)
                 buffers.append(buff)
 
-            ### end for each array
+            # end for each array
 
             spriteToAdd = copy.deepcopy(generatorSprite)
             spriteToAdd.buffers = buffers
@@ -361,6 +347,7 @@ def __resizeSprites(sprites, destSize, imgFormat):
 
     return returnSprites
 
+
 def calculateXYDimensions(frame):
     if len(frame.shape) != 3:
         raise ValueError('frame must have the dimension 3')
@@ -373,17 +360,18 @@ def calculateXYDimensions(frame):
     pixel_offset = [0, 0]
 
     if new_width < max_size:
-      pixel_offset[0] = math.ceil((max_size - new_width) / 2)
-      new_width = max_size
+        pixel_offset[0] = math.ceil((max_size - new_width) / 2)
+        new_width = max_size
 
     if new_height < max_size:
-      pixel_offset[1] = math.ceil((max_size - new_height) / 2)
-      new_height = max_size
+        pixel_offset[1] = math.ceil((max_size - new_height) / 2)
+        new_height = max_size
 
     logger.debug('sliceMapCreator pixeloffsets %d, %d, newWidth %d' % (pixel_offset[0], pixel_offset[1], new_width))
 
     return pixel_offset, (new_width, new_height)
 
+
 def crop_frames(frames, pixel_offset, new_size):
     if len(frames.shape) != 4:
         raise ValueError('frame must have the dimension 3')
@@ -397,22 +385,24 @@ def crop_frames(frames, pixel_offset, new_size):
 
     logger.debug('squared_frames.shape: %d, %d, %d, %d' % squared_frames.shape)
     logger.debug('        frames.shape: %d, %d, %d, %d' % frames.shape)
-    logger.debug('offsety: %d, offsetx: %d ' %(offset_y, offset_x))
+    logger.debug('offsety: %d, offsetx: %d ' % (offset_y, offset_x))
     '''for frameNumber in range(0, frames.shape[0]):
         squared_frames[frameNumber] = sliceMapCreator.cropFrame(frames[frameNumber], pixelOffset, newSize)'''
 
-    squared_frames[:, :, offset_y : y + offset_y, offset_x : x + offset_x ] = frames
+    squared_frames[:, :, offset_y: y + offset_y, offset_x: x + offset_x] = frames
 
     '''newFrame = np.zeros((z, y + 2 * offset_y, x + 2 * offset_x), dtype=frame.dtype)
     newFrame[:, offset_y : offset_y + y, offset_x : offset_x + x]'''
 
     return squared_frames
 
+
 class ResultFrame():
     def __init__(self, frame, fromImage):
         self.frame = frame
         self.fromImage = fromImage
 
+
 def framePreprocessor(inFrame, queue, fromImage, toImage, destShape):
     numberOfImages = toImage - fromImage + 1
     outFrame = np.empty((numberOfImages, destShape[0], destShape[1]), dtype=inFrame.dtype)

imageprocessing/tiffPreparer.py

@@ -1,15 +1,12 @@
-import io, os, sys, errno
+import os
 import re
-import argparse
 import glob
 
 import numpy as np
 
 from django.conf import settings
 
-from skimage.transform import resize
 from skimage.io import imread
-from skimage.io import imsave
 from skimage.io import ImageCollection
 from skimage import img_as_ubyte
 
@@ -23,12 +20,11 @@ import logging
 
 logger = logging.getLogger(__name__)
 
-import pdb
 
 def processTiffFile(filepath):
     # ends with tif* check
     if re.search('.tif(f)?$', filepath) is None:
-        raise ValueError('no tif(f) file given, given filename was "%s"' % filename)
+        raise ValueError('no tif(f) file given, given filename was "%s"' % filepath)
 
     logger.debug('tiffPreparer: reading file: "%s"' % filepath)
     inputFile = imread(filepath, plugin='tifffile')
@@ -61,7 +57,7 @@ def processTiffFile(filepath):
             returnCode = subprocess.call(fJCmd, shell=True)
             logger.debug('tiffPreparer: returnCode ' + str(returnCode))
             if returnCode != 0:
-                raise Error('please refer to logs')
+                raise Exception('please refer to logs')
 
             collection = ImageCollection(sequencePath + '*.tif')
             images = collection.concatenate()
@@ -80,11 +76,13 @@ def processTiffFile(filepath):
 
     return inputFile
 
+
 def imread_convert(f):
     image = imread(f, plugin='tifffile')
 
     return img_as_ubyte(image)
 
+
 def prepareImageSequence(path):
     filenames = sorted(glob.glob(os.path.join(path, '*.tif*')))
     z = len(filenames)