diff options
Diffstat (limited to 'silx/third_party')
| -rw-r--r-- | silx/third_party/EdfFile.py | 1225 | ||||
| -rw-r--r-- | silx/third_party/TiffIO.py | 1268 | ||||
| -rw-r--r-- | silx/third_party/__init__.py | 33 | ||||
| -rw-r--r-- | silx/third_party/scipy_spatial.py | 51 | ||||
| -rw-r--r-- | silx/third_party/setup.py | 49 |
5 files changed, 0 insertions, 2626 deletions
diff --git a/silx/third_party/EdfFile.py b/silx/third_party/EdfFile.py deleted file mode 100644 index 0606d1c..0000000 --- a/silx/third_party/EdfFile.py +++ /dev/null @@ -1,1225 +0,0 @@ -# /*########################################################################## -# -# Copyright (c) 2004-2020 European Synchrotron Radiation Facility -# -# This file is part of the PyMca X-ray Fluorescence Toolkit developed at -# the ESRF by the Software group. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# ############################################################################*/ -__author__ = "Alexandre Gobbo, V.A. Sole - ESRF Data Analysis" -__contact__ = "sole@esrf.fr" -__license__ = "MIT" -__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" -""" - EdfFile.py - Generic class for Edf files manipulation. - - Interface: - =========================== - class EdfFile: - __init__(self,FileName) - GetNumImages(self) - def GetData(self,Index, DataType="",Pos=None,Size=None): - GetPixel(self,Index,Position) - GetHeader(self,Index) - GetStaticHeader(self,Index) - WriteImage (self,Header,Data,Append=1,DataType="",WriteAsUnsigened=0,ByteOrder="") - - - Edf format assumptions: - =========================== - The following details were assumed for this implementation: - - Each Edf file contains a certain number of data blocks. - - Each data block represents data stored in an one, two or three-dimensional array. - - Each data block contains a header section, written in ASCII, and a data section of - binary information. - - The size of the header section in bytes is a multiple of 1024. The header is - padded with spaces (0x20). If the header is not padded to a multiple of 1024, - the file is recognized, but the output is always made in this format. - - The header section starts by '{' and finishes by '}'. It is composed by several - pairs 'keyword = value;'. The keywords are case insensitive, but the values are case - sensitive. Each pair is put in a new line (they are separeted by 0x0A). In the - end of each line, a semicolon (;) separes the pair of a comment, not interpreted. - Exemple: - { - ; Exemple Header - HeaderID = EH:000001:000000:000000 ; automatically generated - ByteOrder = LowByteFirst ; - DataType = FloatValue ; 4 bytes per pixel - Size = 4000000 ; size of data section - Dim_1= 1000 ; x coordinates - Dim_2 = 1000 ; y coordinates - - (padded with spaces to complete 1024 bytes) - } - - There are some fields in the header that are required for this implementation. If any of - these is missing, or inconsistent, it will be generated an error: - Size: Represents size of data block - Dim_1: size of x coordinates (Dim_2 for 2-dimentional images, and also Dim_3 for 3d) - DataType - ByteOrder - - For the written images, these fields are automatically genereted: - Size,Dim_1 (Dim_2 and Dim_3, if necessary), Byte Order, DataType, HeaderID and Image - These fields are called here "static header", and can be retrieved by the method - GetStaticHeader. Other header components are taken by GetHeader. Both methods returns - a dictionary in which the key is the keyword of the pair. When writting an image through - WriteImage method, the Header parameter should not contain the static header information, - which is automatically generated. - - The indexing of images through these functions is based just on the 0-based position in - the file, the header items HeaderID and Image are not considered for referencing the - images. - - The data section contais a number of bytes equal to the value of Size keyword. Data - section is going to be translated into an 1D, 2D or 3D Numpy Array, and accessed - through GetData method call. -""" -DEBUG = 0 -################################################################################ -import sys -import numpy -import os.path -try: - import gzip - GZIP = True -except: - GZIP = False -try: - import bz2 - BZ2 = True -except: - BZ2 = False - -MARCCD_SUPPORT = False -PILATUS_CBF_SUPPORT = False -CAN_USE_FASTEDF = False - -# Using local TiffIO -from . import TiffIO -TIFF_SUPPORT = True - -# Constants - -HEADER_BLOCK_SIZE = 1024 -STATIC_HEADER_ELEMENTS = ( - "HeaderID", - "Image", - "ByteOrder", - "DataType", - "Dim_1", - "Dim_2", - "Dim_3", - "Offset_1", - "Offset_2", - "Offset_3", - "Size") - -STATIC_HEADER_ELEMENTS_CAPS = ( - "HEADERID", - "IMAGE", - "BYTEORDER", - "DATATYPE", - "DIM_1", - "DIM_2", - "DIM_3", - "OFFSET_1", - "OFFSET_2", - "OFFSET_3", - "SIZE") - -LOWER_CASE = 0 -UPPER_CASE = 1 - -KEYS = 1 -VALUES = 2 - - -class Image(object): - """ - """ - def __init__(self): - """ Constructor - """ - self.Header = {} - self.StaticHeader = {} - self.HeaderPosition = 0 - self.DataPosition = 0 - self.Size = 0 - self.NumDim = 1 - self.Dim1 = 0 - self.Dim2 = 0 - self.Dim3 = 0 - self.DataType = "" - - -class EdfFile(object): - """ - """ - def __init__(self, FileName, access=None, fastedf=None): - """ Constructor - - :param FileName: Name of the file (either existing or to be created) - :type FileName: string - :param access: access mode "r" for reading (the file should exist) or - "w" for writing (if the file does not exist, it does not matter). - :type access: string - :type fastedf: True to use the fastedf module - :param fastedf: bool - """ - self.Images = [] - self.NumImages = 0 - self.FileName = FileName - self.File = 0 - if fastedf is None: - fastedf = 0 - self.fastedf = fastedf - self.ADSC = False - self.MARCCD = False - self.TIFF = False - self.PILATUS_CBF = False - self.SPE = False - if sys.byteorder == "big": - self.SysByteOrder = "HighByteFirst" - else: - self.SysByteOrder = "LowByteFirst" - - if hasattr(FileName, "seek") and\ - hasattr(FileName, "read"): - # this looks like a file descriptor ... - self.__ownedOpen = False - self.File = FileName - try: - self.FileName = self.File.name - except AttributeError: - self.FileName = self.File.filename - elif FileName.lower().endswith('.gz'): - if GZIP: - self.__ownedOpen = False - self.File = gzip.GzipFile(FileName) - else: - raise IOError("No gzip module support in this system") - elif FileName.lower().endswith('.bz2'): - if BZ2: - self.__ownedOpen = False - self.File = bz2.BZ2File(FileName) - else: - raise IOError("No bz2 module support in this system") - else: - self.__ownedOpen = True - - if self.File in [0, None]: - if access is not None: - if access[0].upper() == "R": - if not os.path.isfile(self.FileName): - raise IOError("File %s not found" % FileName) - if 'b' not in access: - access += 'b' - if 1: - if not os.path.isfile(self.FileName): - # write access - if access is None: - # allow writing and reading - access = "ab+" - self.File = open(self.FileName, access) - self.File.seek(0, 0) - return - if 'b' not in access: - access += 'b' - self.File = open(self.FileName, access) - return - else: - if access is None: - if (os.access(self.FileName, os.W_OK)): - access = "r+b" - else: - access = "rb" - self.File = open(self.FileName, access) - self.File.seek(0, 0) - twoChars = self.File.read(2) - tiff = False - if sys.version < '3.0': - if twoChars in ["II", "MM"]: - tiff = True - elif twoChars in [eval('b"II"'), eval('b"MM"')]: - tiff = True - if tiff: - fileExtension = os.path.splitext(self.FileName)[-1] - if fileExtension.lower() in [".tif", ".tiff"] or\ - sys.version > '2.9': - if not TIFF_SUPPORT: - raise IOError("TIFF support not implemented") - else: - self.TIFF = True - elif not MARCCD_SUPPORT: - if not TIFF_SUPPORT: - raise IOError("MarCCD support not implemented") - else: - self.TIFF = True - else: - self.MARCCD = True - basename = os.path.basename(FileName).upper() - if basename.endswith('.CBF'): - if not PILATUS_CBF_SUPPORT: - raise IOError("CBF support not implemented") - if twoChars[0] != "{": - self.PILATUS_CBF = True - elif basename.endswith('.SPE'): - if twoChars[0] != "$": - self.SPE = True - elif basename.endswith('EDF.GZ') or basename.endswith('CCD.GZ'): - self.GZIP = True - else: - try: - self.File.close() - except: - pass - raise IOError("EdfFile: Error opening file") - - self.File.seek(0, 0) - if self.TIFF: - self._wrapTIFF() - self.File.close() - return - if self.MARCCD: - self._wrapMarCCD() - self.File.close() - return - if self.PILATUS_CBF: - self._wrapPilatusCBF() - self.File.close() - return - if self.SPE: - self._wrapSPE() - self.File.close() - return - - Index = 0 - line = self.File.readline() - selectedLines = [""] - if sys.version > '2.6': - selectedLines.append(eval('b""')) - parsingHeader = False - while line not in selectedLines: - # decode to make sure I have character string - # str to make sure python 2.x sees it as string and not unicode - if sys.version < '3.0': - if type(line) != type(str("")): - line = "%s" % line - else: - try: - line = str(line.decode()) - except UnicodeDecodeError: - try: - line = str(line.decode('utf-8')) - except UnicodeDecodeError: - try: - line = str(line.decode('latin-1')) - except UnicodeDecodeError: - line = "%s" % line - if (line.count("{\n") >= 1) or (line.count("{\r\n") >= 1): - parsingHeader = True - Index = self.NumImages - self.NumImages = self.NumImages + 1 - self.Images.append(Image()) - - if line.count("=") >= 1: - listItems = line.split("=", 1) - typeItem = listItems[0].strip() - listItems = listItems[1].split(";", 1) - valueItem = listItems[0].strip() - if (typeItem == "HEADER_BYTES") and (Index == 0): - self.ADSC = True - break - - # if typeItem in self.Images[Index].StaticHeader.keys(): - if typeItem.upper() in STATIC_HEADER_ELEMENTS_CAPS: - self.Images[Index].StaticHeader[typeItem] = valueItem - else: - self.Images[Index].Header[typeItem] = valueItem - if ((line.count("}\n") >= 1) or (line.count("}\r") >= 1)) and (parsingHeader): - parsingHeader = False - # for i in STATIC_HEADER_ELEMENTS_CAPS: - # if self.Images[Index].StaticHeader[i]=="": - # raise "Bad File Format" - self.Images[Index].DataPosition = self.File.tell() - # self.File.seek(int(self.Images[Index].StaticHeader["Size"]), 1) - StaticPar = SetDictCase(self.Images[Index].StaticHeader, UPPER_CASE, KEYS) - if "SIZE" in StaticPar.keys(): - self.Images[Index].Size = int(StaticPar["SIZE"]) - if self.Images[Index].Size <= 0: - self.NumImages = Index - line = self.File.readline() - continue - else: - raise TypeError("EdfFile: Image doesn't have size information") - if "DIM_1" in StaticPar.keys(): - self.Images[Index].Dim1 = int(StaticPar["DIM_1"]) - self.Images[Index].Offset1 = int(StaticPar.get("Offset_1", "0")) - else: - raise TypeError("EdfFile: Image doesn't have dimension information") - if "DIM_2" in StaticPar.keys(): - self.Images[Index].NumDim = 2 - self.Images[Index].Dim2 = int(StaticPar["DIM_2"]) - self.Images[Index].Offset2 = int(StaticPar.get("Offset_2", "0")) - if "DIM_3" in StaticPar.keys(): - self.Images[Index].NumDim = 3 - self.Images[Index].Dim3 = int(StaticPar["DIM_3"]) - self.Images[Index].Offset3 = int(StaticPar.get("Offset_3", "0")) - if "DATATYPE" in StaticPar.keys(): - self.Images[Index].DataType = StaticPar["DATATYPE"] - else: - raise TypeError("EdfFile: Image doesn't have datatype information") - if "BYTEORDER" in StaticPar.keys(): - self.Images[Index].ByteOrder = StaticPar["BYTEORDER"] - else: - raise TypeError("EdfFile: Image doesn't have byteorder information") - - self.File.seek(self.Images[Index].Size, 1) - - line = self.File.readline() - - if self.ADSC: - self.File.seek(0, 0) - self.NumImages = 1 - # this is a bad implementation of fabio adscimage - # please take a look at the fabio module of fable at sourceforge - infile = self.File - header_keys = [] - header = {} - try: - """ read an adsc header """ - line = infile.readline() - bytesread = len(line) - while '}' not in line: - if '=' in line: - (key, val) = line.split('=') - header_keys.append(key.strip()) - header[key.strip()] = val.strip(' ;\n') - line = infile.readline() - bytesread = bytesread + len(line) - except: - raise Exception("Error processing adsc header") - # banned by bzip/gzip??? - try: - infile.seek(int(header['HEADER_BYTES']), 0) - except TypeError: - # Gzipped does not allow a seek and read header is not - # promising to stop in the right place - infile.close() - infile = self._open(fname, "rb") - infile.read(int(header['HEADER_BYTES'])) - binary = infile.read() - infile.close() - - # now read the data into the array - self.Images[Index].Dim1 = int(header['SIZE1']) - self.Images[Index].Dim2 = int(header['SIZE2']) - self.Images[Index].NumDim = 2 - self.Images[Index].DataType = 'UnsignedShort' - try: - self.__data = numpy.reshape( - numpy.copy(numpy.frombuffer(binary, numpy.uint16)), - (self.Images[Index].Dim2, self.Images[Index].Dim1)) - except ValueError: - msg = 'Size spec in ADSC-header does not match size of image data field' - raise IOError(msg) - if 'little' in header['BYTE_ORDER']: - self.Images[Index].ByteOrder = 'LowByteFirst' - else: - self.Images[Index].ByteOrder = 'HighByteFirst' - if self.SysByteOrder.upper() != self.Images[Index].ByteOrder.upper(): - self.__data = self.__data.byteswap() - self.Images[Index].ByteOrder = self.SysByteOrder - - self.Images[Index].StaticHeader['Dim_1'] = self.Images[Index].Dim1 - self.Images[Index].StaticHeader['Dim_2'] = self.Images[Index].Dim2 - self.Images[Index].StaticHeader['Offset_1'] = 0 - self.Images[Index].StaticHeader['Offset_2'] = 0 - self.Images[Index].StaticHeader['DataType'] = self.Images[Index].DataType - - self.__makeSureFileIsClosed() - - def _wrapTIFF(self): - self._wrappedInstance = TiffIO.TiffIO(self.File, cache_length=0, mono_output=True) - self.NumImages = self._wrappedInstance.getNumberOfImages() - if self.NumImages < 1: - return - - # wrapped image objects have to provide getInfo and getData - # info = self._wrappedInstance.getInfo( index) - # data = self._wrappedInstance.getData( index) - # for the time being I am going to assume all the images - # in the file have the same data type type - data = None - - for Index in range(self.NumImages): - info = self._wrappedInstance.getInfo(Index) - self.Images.append(Image()) - self.Images[Index].Dim1 = info['nRows'] - self.Images[Index].Dim2 = info['nColumns'] - self.Images[Index].NumDim = 2 - if data is None: - data = self._wrappedInstance.getData(0) - self.Images[Index].DataType = self.__GetDefaultEdfType__(data.dtype) - self.Images[Index].StaticHeader['Dim_1'] = self.Images[Index].Dim1 - self.Images[Index].StaticHeader['Dim_2'] = self.Images[Index].Dim2 - self.Images[Index].StaticHeader['Offset_1'] = 0 - self.Images[Index].StaticHeader['Offset_2'] = 0 - self.Images[Index].StaticHeader['DataType'] = self.Images[Index].DataType - self.Images[Index].Header.update(info) - - def _wrapMarCCD(self): - raise NotImplementedError("Look at the module EdfFile from PyMca") - - def _wrapPilatusCBF(self): - raise NotImplementedError("Look at the module EdfFile from PyMca") - - def _wrapSPE(self): - if 0 and sys.version < '3.0': - self.File.seek(42) - xdim = numpy.int64(numpy.fromfile(self.File, numpy.int16, 1)[0]) - self.File.seek(656) - ydim = numpy.int64(numpy.fromfile(self.File, numpy.int16, 1)) - self.File.seek(4100) - self.__data = numpy.fromfile(self.File, numpy.uint16, int(xdim * ydim)) - else: - import struct - self.File.seek(0) - a = self.File.read() - xdim = numpy.int64(struct.unpack('<h', a[42:44])[0]) - ydim = numpy.int64(struct.unpack('<h', a[656:658])[0]) - fmt = '<%dH' % int(xdim * ydim) - self.__data = numpy.array(struct.unpack(fmt, a[4100:int(4100 + int(2 * xdim * ydim))])).astype(numpy.uint16) - self.__data.shape = ydim, xdim - Index = 0 - self.Images.append(Image()) - self.NumImages = 1 - self.Images[Index].Dim1 = ydim - self.Images[Index].Dim2 = xdim - self.Images[Index].NumDim = 2 - self.Images[Index].DataType = 'UnsignedShort' - self.Images[Index].ByteOrder = 'LowByteFirst' - if self.SysByteOrder.upper() != self.Images[Index].ByteOrder.upper(): - self.__data = self.__data.byteswap() - self.Images[Index].StaticHeader['Dim_1'] = self.Images[Index].Dim1 - self.Images[Index].StaticHeader['Dim_2'] = self.Images[Index].Dim2 - self.Images[Index].StaticHeader['Offset_1'] = 0 - self.Images[Index].StaticHeader['Offset_2'] = 0 - self.Images[Index].StaticHeader['DataType'] = self.Images[Index].DataType - - def GetNumImages(self): - """ Returns number of images of the object (and associated file) - """ - return self.NumImages - - def GetData(self, *var, **kw): - try: - self.__makeSureFileIsOpen() - return self._GetData(*var, **kw) - finally: - self.__makeSureFileIsClosed() - - def _GetData(self, Index, DataType="", Pos=None, Size=None): - """ Returns numpy array with image data - Index: The zero-based index of the image in the file - DataType: The edf type of the array to be returnd - If ommited, it is used the default one for the type - indicated in the image header - Attention to the absence of UnsignedShort, - UnsignedInteger and UnsignedLong types in - Numpy Python - Default relation between Edf types and NumPy's typecodes: - SignedByte int8 b - UnsignedByte uint8 B - SignedShort int16 h - UnsignedShort uint16 H - SignedInteger int32 i - UnsignedInteger uint32 I - SignedLong int32 i - UnsignedLong uint32 I - Signed64 int64 (l in 64bit, q in 32 bit) - Unsigned64 uint64 (L in 64bit, Q in 32 bit) - FloatValue float32 f - DoubleValue float64 d - Pos: Tuple (x) or (x,y) or (x,y,z) that indicates the begining - of data to be read. If ommited, set to the origin (0), - (0,0) or (0,0,0) - Size: Tuple, size of the data to be returned as x) or (x,y) or - (x,y,z) if ommited, is the distance from Pos to the end. - - If Pos and Size not mentioned, returns the whole data. - """ - fastedf = self.fastedf - if Index < 0 or Index >= self.NumImages: - raise ValueError("EdfFile: Index out of limit") - if fastedf is None: - fastedf = 0 - if Pos is None and Size is None: - if self.ADSC or self.MARCCD or self.PILATUS_CBF or self.SPE: - return self.__data - elif self.TIFF: - data = self._wrappedInstance.getData(Index) - return data - else: - self.File.seek(self.Images[Index].DataPosition, 0) - datatype = self.__GetDefaultNumpyType__(self.Images[Index].DataType, index=Index) - try: - datasize = self.__GetSizeNumpyType__(datatype) - except TypeError: - print("What is the meaning of this error?") - datasize = 8 - if self.Images[Index].NumDim == 3: - image = self.Images[Index] - sizeToRead = image.Dim1 * image.Dim2 * image.Dim3 * datasize - Data = numpy.copy(numpy.frombuffer(self.File.read(sizeToRead), datatype)) - Data = numpy.reshape(Data, (self.Images[Index].Dim3, self.Images[Index].Dim2, self.Images[Index].Dim1)) - elif self.Images[Index].NumDim == 2: - image = self.Images[Index] - sizeToRead = image.Dim1 * image.Dim2 * datasize - Data = numpy.copy(numpy.frombuffer(self.File.read(sizeToRead), datatype)) - # print "datatype = ",datatype - # print "Data.type = ", Data.dtype.char - # print "self.Images[Index].DataType ", self.Images[Index].DataType - # print "Data.shape",Data.shape - # print "datasize = ",datasize - # print "sizeToRead ",sizeToRead - # print "lenData = ", len(Data) - Data = numpy.reshape(Data, (self.Images[Index].Dim2, self.Images[Index].Dim1)) - elif self.Images[Index].NumDim == 1: - sizeToRead = self.Images[Index].Dim1 * datasize - Data = numpy.copy(numpy.frombuffer(self.File.read(sizeToRead), datatype)) - elif self.ADSC or self.MARCCD or self.PILATUS_CBF or self.SPE: - return self.__data[Pos[1]:(Pos[1] + Size[1]), - Pos[0]:(Pos[0] + Size[0])] - elif self.TIFF: - data = self._wrappedInstance.getData(Index) - return data[Pos[1]:(Pos[1] + Size[1]), Pos[0]:(Pos[0] + Size[0])] - elif fastedf and CAN_USE_FASTEDF: - raise NotImplementedError("Look at the module EdfFile from PyMCA") - else: - if fastedf: - print("It could not use fast routines") - type_ = self.__GetDefaultNumpyType__(self.Images[Index].DataType, index=Index) - size_pixel = self.__GetSizeNumpyType__(type_) - Data = numpy.array([], type_) - if self.Images[Index].NumDim == 1: - if Pos is None: - Pos = (0,) - if Size is None: - Size = (0,) - sizex = self.Images[Index].Dim1 - Size = list(Size) - if Size[0] == 0: - Size[0] = sizex - Pos[0] - self.File.seek((Pos[0] * size_pixel) + self.Images[Index].DataPosition, 0) - Data = numpy.copy(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_)) - elif self.Images[Index].NumDim == 2: - if Pos is None: - Pos = (0, 0) - if Size is None: - Size = (0, 0) - Size = list(Size) - sizex, sizey = self.Images[Index].Dim1, self.Images[Index].Dim2 - if Size[0] == 0: - Size[0] = sizex - Pos[0] - if Size[1] == 0: - Size[1] = sizey - Pos[1] - # print len(range(Pos[1],Pos[1]+Size[1])), "LECTURES OF ", Size[0], "POINTS" - # print "sizex = ", sizex, "sizey = ", sizey - Data = numpy.zeros((Size[1], Size[0]), type_) - dataindex = 0 - for y in range(Pos[1], Pos[1] + Size[1]): - self.File.seek((((y * sizex) + Pos[0]) * size_pixel) + self.Images[Index].DataPosition, 0) - line = numpy.copy(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_)) - Data[dataindex, :] = line[:] - # Data=numpy.concatenate((Data,line)) - dataindex += 1 - # print "DataSize = ",Data.shape - # print "Requested reshape = ",Size[1],'x',Size[0] - # Data = numpy.reshape(Data, (Size[1],Size[0])) - elif self.Images[Index].NumDim == 3: - if Pos is None: - Pos = (0, 0, 0) - if Size is None: - Size = (0, 0, 0) - Size = list(Size) - sizex, sizey, sizez = self.Images[Index].Dim1, self.Images[Index].Dim2, self.Images[Index].Dim3 - if Size[0] == 0: - Size[0] = sizex - Pos[0] - if Size[1] == 0: - Size[1] = sizey - Pos[1] - if Size[2] == 0: - Size[2] = sizez - Pos[2] - for z in range(Pos[2], Pos[2] + Size[2]): - for y in range(Pos[1], Pos[1] + Size[1]): - self.File.seek(((((z * sizey + y) * sizex) + Pos[0]) * size_pixel) + self.Images[Index].DataPosition, 0) - line = numpy.copy(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_)) - Data = numpy.concatenate((Data, line)) - Data = numpy.reshape(Data, (Size[2], Size[1], Size[0])) - - if self.SysByteOrder.upper() != self.Images[Index].ByteOrder.upper(): - Data = Data.byteswap() - if DataType != "": - Data = self.__SetDataType__(Data, DataType) - return Data - - def GetPixel(self, Index, Position): - """ Returns double value of the pixel, regardless the format of the array - Index: The zero-based index of the image in the file - Position: Tuple with the coordinete (x), (x,y) or (x,y,z) - """ - if Index < 0 or Index >= self.NumImages: - raise ValueError("EdfFile: Index out of limit") - if len(Position) != self.Images[Index].NumDim: - raise ValueError("EdfFile: coordinate with wrong dimension ") - - size_pixel = self.__GetSizeNumpyType__(self.__GetDefaultNumpyType__(self.Images[Index].DataType, index=Index)) - offset = Position[0] * size_pixel - if self.Images[Index].NumDim > 1: - size_row = size_pixel * self.Images[Index].Dim1 - offset = offset + (Position[1] * size_row) - if self.Images[Index].NumDim == 3: - size_img = size_row * self.Images[Index].Dim2 - offset = offset + (Position[2] * size_img) - self.File.seek(self.Images[Index].DataPosition + offset, 0) - Data = numpy.copy(numpy.frombuffer(self.File.read(size_pixel), - self.__GetDefaultNumpyType__(self.Images[Index].DataType, - index=Index))) - if self.SysByteOrder.upper() != self.Images[Index].ByteOrder.upper(): - Data = Data.byteswap() - Data = self.__SetDataType__(Data, "DoubleValue") - return Data[0] - - def GetHeader(self, Index): - """ Returns dictionary with image header fields. - Does not include the basic fields (static) defined by data shape, - type and file position. These are get with GetStaticHeader - method. - Index: The zero-based index of the image in the file - """ - if Index < 0 or Index >= self.NumImages: - raise ValueError("Index out of limit") - # return self.Images[Index].Header - ret = {} - for i in self.Images[Index].Header.keys(): - ret[i] = self.Images[Index].Header[i] - return ret - - def GetStaticHeader(self, Index): - """ Returns dictionary with static parameters - Data format and file position dependent information - (dim1,dim2,size,datatype,byteorder,headerId,Image) - Index: The zero-based index of the image in the file - """ - if Index < 0 or Index >= self.NumImages: - raise ValueError("Index out of limit") - # return self.Images[Index].StaticHeader - ret = {} - for i in self.Images[Index].StaticHeader.keys(): - ret[i] = self.Images[Index].StaticHeader[i] - return ret - - def WriteImage(self, *var, **kw): - try: - self.__makeSureFileIsOpen() - return self._WriteImage(*var, **kw) - finally: - self.__makeSureFileIsClosed() - - def _WriteImage(self, Header, Data, Append=1, DataType="", ByteOrder=""): - """ Writes image to the file. - Header: Dictionary containing the non-static header - information (static information is generated - according to position of image and data format - Append: If equals to 0, overwrites the file. Otherwise, appends - to the end of the file - DataType: The data type to be saved to the file: - SignedByte - UnsignedByte - SignedShort - UnsignedShort - SignedInteger - UnsignedInteger - SignedLong - UnsignedLong - FloatValue - DoubleValue - Default: according to Data array typecode: - 1: SignedByte - b: UnsignedByte - s: SignedShort - w: UnsignedShort - i: SignedInteger - l: SignedLong - u: UnsignedLong - f: FloatValue - d: DoubleValue - ByteOrder: Byte order of the data in file: - HighByteFirst - LowByteFirst - Default: system's byte order - """ - if Append == 0: - self.File.truncate(0) - self.Images = [] - self.NumImages = 0 - Index = self.NumImages - self.NumImages = self.NumImages + 1 - self.Images.append(Image()) - - # self.Images[Index].StaticHeader["Dim_1"] = "%d" % Data.shape[1] - # self.Images[Index].StaticHeader["Dim_2"] = "%d" % Data.shape[0] - scalarSize = self.__GetSizeNumpyType__(Data.dtype) - if len(Data.shape) == 1: - self.Images[Index].Dim1 = Data.shape[0] - self.Images[Index].StaticHeader["Dim_1"] = "%d" % self.Images[Index].Dim1 - self.Images[Index].Size = Data.shape[0] * scalarSize - elif len(Data.shape) == 2: - self.Images[Index].Dim1 = Data.shape[1] - self.Images[Index].Dim2 = Data.shape[0] - self.Images[Index].StaticHeader["Dim_1"] = "%d" % self.Images[Index].Dim1 - self.Images[Index].StaticHeader["Dim_2"] = "%d" % self.Images[Index].Dim2 - self.Images[Index].Size = Data.shape[0] * Data.shape[1] * scalarSize - self.Images[Index].NumDim = 2 - elif len(Data.shape) == 3: - self.Images[Index].Dim1 = Data.shape[2] - self.Images[Index].Dim2 = Data.shape[1] - self.Images[Index].Dim3 = Data.shape[0] - self.Images[Index].StaticHeader["Dim_1"] = "%d" % self.Images[Index].Dim1 - self.Images[Index].StaticHeader["Dim_2"] = "%d" % self.Images[Index].Dim2 - self.Images[Index].StaticHeader["Dim_3"] = "%d" % self.Images[Index].Dim3 - self.Images[Index].Size = Data.shape[0] * Data.shape[1] * Data.shape[2] * scalarSize - self.Images[Index].NumDim = 3 - elif len(Data.shape) > 3: - raise TypeError("EdfFile: Data dimension not suported") - - if DataType == "": - self.Images[Index].DataType = self.__GetDefaultEdfType__(Data.dtype) - else: - self.Images[Index].DataType = DataType - Data = self.__SetDataType__(Data, DataType) - - if ByteOrder == "": - self.Images[Index].ByteOrder = self.SysByteOrder - else: - self.Images[Index].ByteOrder = ByteOrder - - self.Images[Index].StaticHeader["Size"] = "%d" % self.Images[Index].Size - self.Images[Index].StaticHeader["Image"] = Index + 1 - self.Images[Index].StaticHeader["HeaderID"] = "EH:%06d:000000:000000" % self.Images[Index].StaticHeader["Image"] - self.Images[Index].StaticHeader["ByteOrder"] = self.Images[Index].ByteOrder - self.Images[Index].StaticHeader["DataType"] = self.Images[Index].DataType - - self.Images[Index].Header = {} - self.File.seek(0, 2) - StrHeader = "{\n" - for i in STATIC_HEADER_ELEMENTS: - if i in self.Images[Index].StaticHeader.keys(): - StrHeader = StrHeader + ("%s = %s ;\n" % (i, self.Images[Index].StaticHeader[i])) - for i in Header.keys(): - StrHeader = StrHeader + ("%s = %s ;\n" % (i, Header[i])) - self.Images[Index].Header[i] = Header[i] - newsize = (((len(StrHeader) + 1) // HEADER_BLOCK_SIZE) + 1) * HEADER_BLOCK_SIZE - 2 - newsize = int(newsize) - StrHeader = StrHeader.ljust(newsize) - StrHeader = StrHeader + "}\n" - - self.Images[Index].HeaderPosition = self.File.tell() - self.File.write(StrHeader.encode()) - self.Images[Index].DataPosition = self.File.tell() - - # if self.Images[Index].StaticHeader["ByteOrder"] != self.SysByteOrder: - if self.Images[Index].ByteOrder.upper() != self.SysByteOrder.upper(): - self.File.write((Data.byteswap()).tobytes()) - else: - self.File.write(Data.tobytes()) - - def __makeSureFileIsOpen(self): - if DEBUG: - print("Making sure file is open") - if not self.__ownedOpen: - return - if self.ADSC or self.MARCCD or self.PILATUS_CBF or self.SPE: - if DEBUG: - print("Special case. Image is buffered") - return - if self.File in [0, None]: - if DEBUG: - print("File is None") - elif self.File.closed: - if DEBUG: - print("Reopening closed file") - accessMode = self.File.mode - fileName = self.File.name - newFile = open(fileName, accessMode) - self.File = newFile - return - - def __makeSureFileIsClosed(self): - if DEBUG: - print("Making sure file is closed") - if not self.__ownedOpen: - return - if self.ADSC or self.MARCCD or self.PILATUS_CBF or self.SPE: - if DEBUG: - print("Special case. Image is buffered") - return - if self.File in [0, None]: - if DEBUG: - print("File is None") - elif not self.File.closed: - if DEBUG: - print("Closing file") - self.File.close() - return - - def __GetDefaultNumpyType__(self, EdfType, index=None): - """ Internal method: returns NumPy type according to Edf type - """ - return self.GetDefaultNumpyType(EdfType, index) - - def __GetDefaultEdfType__(self, NumpyType): - """ Internal method: returns Edf type according Numpy type - """ - if NumpyType in ["b", numpy.int8]: - return "SignedByte" - elif NumpyType in ["B", numpy.uint8]: - return "UnsignedByte" - elif NumpyType in ["h", numpy.int16]: - return "SignedShort" - elif NumpyType in ["H", numpy.uint16]: - return "UnsignedShort" - elif NumpyType in ["i", numpy.int32]: - return "SignedInteger" - elif NumpyType in ["I", numpy.uint32]: - return "UnsignedInteger" - elif NumpyType == "l": - if sys.platform == 'linux2': - return "Signed64" - else: - return "SignedLong" - elif NumpyType == "L": - if sys.platform == 'linux2': - return "Unsigned64" - else: - return "UnsignedLong" - elif NumpyType == numpy.int64: - return "Signed64" - elif NumpyType == numpy.uint64: - return "Unsigned64" - elif NumpyType in ["f", numpy.float32]: - return "FloatValue" - elif NumpyType in ["d", numpy.float64]: - return "DoubleValue" - else: - raise TypeError("unknown NumpyType %s" % NumpyType) - - def __GetSizeNumpyType__(self, NumpyType): - """ Internal method: returns size of NumPy's Array Types - """ - if NumpyType in ["b", numpy.int8]: - return 1 - elif NumpyType in ["B", numpy.uint8]: - return 1 - elif NumpyType in ["h", numpy.int16]: - return 2 - elif NumpyType in ["H", numpy.uint16]: - return 2 - elif NumpyType in ["i", numpy.int32]: - return 4 - elif NumpyType in ["I", numpy.uint32]: - return 4 - elif NumpyType == "l": - if sys.platform == 'linux2': - return 8 # 64 bit - else: - return 4 # 32 bit - elif NumpyType == "L": - if sys.platform == 'linux2': - return 8 # 64 bit - else: - return 4 # 32 bit - elif NumpyType in ["f", numpy.float32]: - return 4 - elif NumpyType in ["d", numpy.float64]: - return 8 - elif NumpyType == "Q": - return 8 # unsigned 64 in 32 bit - elif NumpyType == "q": - return 8 # signed 64 in 32 bit - elif NumpyType == numpy.uint64: - return 8 - elif NumpyType == numpy.int64: - return 8 - else: - raise TypeError("unknown NumpyType %s" % NumpyType) - - def __SetDataType__(self, Array, DataType): - """ Internal method: array type convertion - """ - # AVOID problems not using FromEdfType= Array.dtype.char - FromEdfType = Array.dtype - ToEdfType = self.__GetDefaultNumpyType__(DataType) - if ToEdfType != FromEdfType: - aux = Array.astype(self.__GetDefaultNumpyType__(DataType)) - return aux - return Array - - def __del__(self): - try: - self.__makeSureFileIsClosed() - except: - pass - - def GetDefaultNumpyType(self, EdfType, index=None): - """ Returns NumPy type according Edf type - """ - if index is None: - return GetDefaultNumpyType(EdfType) - EdfType = EdfType.upper() - if EdfType in ['SIGNED64']: - return numpy.int64 - if EdfType in ['UNSIGNED64']: - return numpy.uint64 - if EdfType in ["SIGNEDLONG", "UNSIGNEDLONG"]: - dim1 = 1 - dim2 = 1 - dim3 = 1 - if hasattr(self.Images[index], "Dim1"): - dim1 = self.Images[index].Dim1 - if hasattr(self.Images[index], "Dim2"): - dim2 = self.Images[index].Dim2 - if dim2 <= 0: - dim2 = 1 - if hasattr(self.Images[index], "Dim3"): - dim3 = self.Images[index].Dim3 - if dim3 <= 0: - dim3 = 1 - if hasattr(self.Images[index], "Size"): - size = self.Images[index].Size - if size / (dim1 * dim2 * dim3) == 8: - if EdfType == "UNSIGNEDLONG": - return numpy.uint64 - else: - return numpy.int64 - if EdfType == "UNSIGNEDLONG": - return numpy.uint32 - else: - return numpy.int32 - - return GetDefaultNumpyType(EdfType) - - -def GetDefaultNumpyType(EdfType): - """ Returns NumPy type according Edf type - """ - EdfType = EdfType.upper() - if EdfType == "SIGNEDBYTE": - return numpy.int8 # "b" - elif EdfType == "UNSIGNEDBYTE": - return numpy.uint8 # "B" - elif EdfType == "SIGNEDSHORT": - return numpy.int16 # "h" - elif EdfType == "UNSIGNEDSHORT": - return numpy.uint16 # "H" - elif EdfType == "SIGNEDINTEGER": - return numpy.int32 # "i" - elif EdfType == "UNSIGNEDINTEGER": - return numpy.uint32 # "I" - elif EdfType == "SIGNEDLONG": - return numpy.int32 # "i" #ESRF acquisition is made in 32bit - elif EdfType == "UNSIGNEDLONG": - return numpy.uint32 # "I" #ESRF acquisition is made in 32bit - elif EdfType == "SIGNED64": - return numpy.int64 # "l" - elif EdfType == "UNSIGNED64": - return numpy.uint64 # "L" - elif EdfType == "FLOATVALUE": - return numpy.float32 # "f" - elif EdfType == "FLOAT": - return numpy.float32 # "f" - elif EdfType == "DOUBLEVALUE": - return numpy.float64 # "d" - else: - raise TypeError("unknown EdfType %s" % EdfType) - - -def SetDictCase(Dict, Case, Flag): - """ Returns dictionary with keys and/or values converted into upper or lowercase - Dict: input dictionary - Case: LOWER_CASE, UPPER_CASE - Flag: KEYS, VALUES or KEYS | VALUES - """ - newdict = {} - for i in Dict.keys(): - newkey = i - newvalue = Dict[i] - if Flag & KEYS: - if Case == LOWER_CASE: - newkey = newkey.lower() - else: - newkey = newkey.upper() - if Flag & VALUES: - if Case == LOWER_CASE: - newvalue = newvalue.lower() - else: - newvalue = newvalue.upper() - newdict[newkey] = newvalue - return newdict - - -def GetRegion(Arr, Pos, Size): - """Returns array with refion of Arr. - Arr must be 1d, 2d or 3d - Pos and Size are tuples in the format (x) or (x,y) or (x,y,z) - Both parameters must have the same size as the dimention of Arr - """ - Dim = len(Arr.shape) - if len(Pos) != Dim: - return None - if len(Size) != Dim: - return None - - if (Dim == 1): - SizeX = Size[0] - if SizeX == 0: - SizeX = Arr.shape[0] - Pos[0] - ArrRet = numpy.take(Arr, range(Pos[0], Pos[0] + SizeX)) - elif (Dim == 2): - SizeX = Size[0] - SizeY = Size[1] - if SizeX == 0: - SizeX = Arr.shape[1] - Pos[0] - if SizeY == 0: - SizeY = Arr.shape[0] - Pos[1] - ArrRet = numpy.take(Arr, range(Pos[1], Pos[1] + SizeY)) - ArrRet = numpy.take(ArrRet, range(Pos[0], Pos[0] + SizeX), 1) - elif (Dim == 3): - SizeX = Size[0] - SizeY = Size[1] - SizeZ = Size[2] - if SizeX == 0: - SizeX = Arr.shape[2] - Pos[0] - if SizeY == 0: - SizeX = Arr.shape[1] - Pos[1] - if SizeZ == 0: - SizeZ = Arr.shape[0] - Pos[2] - ArrRet = numpy.take(Arr, range(Pos[2], Pos[2] + SizeZ)) - ArrRet = numpy.take(ArrRet, range(Pos[1], Pos[1] + SizeY), 1) - ArrRet = numpy.take(ArrRet, range(Pos[0], Pos[0] + SizeX), 2) - else: - ArrRet = None - return ArrRet - - -if __name__ == "__main__": - if 1: - a = numpy.zeros((5, 10)) - for i in range(5): - for j in range(10): - a[i, j] = 10 * i + j - edf = EdfFile("armando.edf", access="ab+") - edf.WriteImage({}, a) - del edf # force to close the file - inp = EdfFile("armando.edf") - b = inp.GetData(0) - out = EdfFile("armando2.edf") - out.WriteImage({}, b) - del out # force to close the file - inp2 = EdfFile("armando2.edf") - c = inp2.GetData(0) - print("A SHAPE = ", a.shape) - print("B SHAPE = ", b.shape) - print("C SHAPE = ", c.shape) - for i in range(5): - print("A", a[i, :]) - print("B", b[i, :]) - print("C", c[i, :]) - - x = numpy.arange(100) - x.shape = 5, 20 - for item in ["SignedByte", "UnsignedByte", - "SignedShort", "UnsignedShort", - "SignedLong", "UnsignedLong", - "Signed64", "Unsigned64", - "FloatValue", "DoubleValue"]: - fname = item + ".edf" - if os.path.exists(fname): - os.remove(fname) - towrite = EdfFile(fname) - towrite.WriteImage({}, x, DataType=item, Append=0) - sys.exit(0) - - # Creates object based on file exe.edf - exe = EdfFile("images/test_image.edf") - x = EdfFile("images/test_getdata.edf") - # Gets unsigned short data, storing in an signed long - arr = exe.GetData(0, Pos=(100, 200), Size=(200, 400)) - x.WriteImage({}, arr, 0) - - arr = exe.GetData(0, Pos=(100, 200)) - x.WriteImage({}, arr) - - arr = exe.GetData(0, Size=(200, 400)) - x.WriteImage({}, arr) - - arr = exe.GetData(0) - x.WriteImage({}, arr) - - sys.exit() - - # Creates object based on file exe.edf - exe = EdfFile("images/.edf") - - # Creates long array , filled with 0xFFFFFFFF(-1) - la = numpy.zeros((100, 100)) - la = la - 1 - - # Creates a short array, filled with 0xFFFF - sa = numpy.zeros((100, 100)) - sa = sa + 0xFFFF - sa = sa.astype("s") - - # Writes long array, initializing file (append=0) - exe.WriteImage({}, la, 0, "") - - # Appends short array with new header items - exe.WriteImage({'Name': 'Alexandre', 'Date': '16/07/2001'}, sa) - - # Appends short array, in Edf type unsigned - exe.WriteImage({}, sa, DataType="UnsignedShort") - - # Appends short array, in Edf type unsigned - exe.WriteImage({}, sa, DataType="UnsignedLong") - - # Appends long array as a double, considering unsigned - exe.WriteImage({}, la, DataType="DoubleValue", WriteAsUnsigened=1) - - # Gets unsigned short data, storing in an signed long - ushort = exe.GetData(2, "SignedLong") - - # Makes an operation - ushort = ushort - 0x10 - - # Saves Result as signed long - exe.WriteImage({}, ushort) - - # Saves in the original format (unsigned short) - OldHeader = exe.GetStaticHeader(2) - exe.WriteImage({}, ushort, 1, OldHeader["DataType"]) diff --git a/silx/third_party/TiffIO.py b/silx/third_party/TiffIO.py deleted file mode 100644 index 7526a75..0000000 --- a/silx/third_party/TiffIO.py +++ /dev/null @@ -1,1268 +0,0 @@ -# /*########################################################################## -# -# The PyMca X-Ray Fluorescence Toolkit -# -# Copyright (c) 2004-2020 European Synchrotron Radiation Facility -# -# This file is part of the PyMca X-ray Fluorescence Toolkit developed at -# the ESRF by the Software group. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# ############################################################################*/ -__author__ = "V.A. Sole - ESRF Data Analysis" -__contact__ = "sole@esrf.fr" -__license__ = "MIT" -__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" - -import sys -import os -import struct -import numpy - -DEBUG = 0 -ALLOW_MULTIPLE_STRIPS = False - -TAG_ID = { 256:"NumberOfColumns", # S or L ImageWidth - 257:"NumberOfRows", # S or L ImageHeight - 258:"BitsPerSample", # S Number of bits per component - 259:"Compression", # SHORT (1 - NoCompression, ... - 262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color - 270:"ImageDescription", # ASCII - 273:"StripOffsets", # S or L, for each strip, the byte offset of the strip - 277:"SamplesPerPixel", # SHORT (>=3) only for RGB images - 278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last - 279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression - 305:"Software", # ASCII - 306:"Date", # ASCII - 320:"Colormap", # Colormap of Palette-color Images - 339:"SampleFormat", # SHORT Interpretation of data in each pixel - } - -#TILES ARE TO BE SUPPORTED TOO ... -TAG_NUMBER_OF_COLUMNS = 256 -TAG_NUMBER_OF_ROWS = 257 -TAG_BITS_PER_SAMPLE = 258 -TAG_PHOTOMETRIC_INTERPRETATION = 262 -TAG_COMPRESSION = 259 -TAG_IMAGE_DESCRIPTION = 270 -TAG_STRIP_OFFSETS = 273 -TAG_SAMPLES_PER_PIXEL = 277 -TAG_ROWS_PER_STRIP = 278 -TAG_STRIP_BYTE_COUNTS = 279 -TAG_SOFTWARE = 305 -TAG_DATE = 306 -TAG_COLORMAP = 320 -TAG_SAMPLE_FORMAT = 339 - -FIELD_TYPE = {1:('BYTE', "B"), - 2:('ASCII', "s"), #string ending with binary zero - 3:('SHORT', "H"), - 4:('LONG', "I"), - 5:('RATIONAL',"II"), - 6:('SBYTE', "b"), - 7:('UNDEFINED',"B"), - 8:('SSHORT', "h"), - 9:('SLONG', "i"), - 10:('SRATIONAL',"ii"), - 11:('FLOAT', "f"), - 12:('DOUBLE', "d")} - -FIELD_TYPE_OUT = { 'B': 1, - 's': 2, - 'H': 3, - 'I': 4, - 'II': 5, - 'b': 6, - 'h': 8, - 'i': 9, - 'ii': 10, - 'f': 11, - 'd': 12} - -#sample formats (http://www.awaresystems.be/imaging/tiff/tiffflags/sampleformat.html) -SAMPLE_FORMAT_UINT = 1 -SAMPLE_FORMAT_INT = 2 -SAMPLE_FORMAT_FLOAT = 3 #floating point -SAMPLE_FORMAT_VOID = 4 #undefined data, usually assumed UINT -SAMPLE_FORMAT_COMPLEXINT = 5 -SAMPLE_FORMAT_COMPLEXIEEEFP = 6 - - - -class TiffIO(object): - def __init__(self, filename, mode=None, cache_length=20, mono_output=False): - if mode is None: - mode = 'rb' - if 'b' not in mode: - mode = mode + 'b' - if 'a' in mode.lower(): - raise IOError("Mode %s makes no sense on TIFF files. Consider 'rb+'" % mode) - if ('w' in mode): - if '+' not in mode: - mode += '+' - - if hasattr(filename, "seek") and\ - hasattr(filename, "read"): - fd = filename - self._access = None - else: - #the b is needed for windows and python 3 - fd = open(filename, mode) - self._access = mode - - self._initInternalVariables(fd) - self._maxImageCacheLength = cache_length - self._forceMonoOutput = mono_output - - def _initInternalVariables(self, fd=None): - if fd is None: - fd = self.fd - else: - self.fd = fd - # read the order - fd.seek(0) - order = fd.read(2).decode() - if len(order): - if order == "II": - #intel, little endian - fileOrder = "little" - self._structChar = '<' - elif order == "MM": - #motorola, high endian - fileOrder = "big" - self._structChar = '>' - else: - raise IOError("File is not a Mar CCD file, nor a TIFF file") - a = fd.read(2) - fortyTwo = struct.unpack(self._structChar+"H",a)[0] - if fortyTwo != 42: - raise IOError("Invalid TIFF version %d" % fortyTwo) - else: - if DEBUG: - print("VALID TIFF VERSION") - if sys.byteorder != fileOrder: - swap = True - else: - swap = False - else: - if sys.byteorder == "little": - self._structChar = '<' - else: - self._structChar = '>' - swap = False - self._swap = swap - self._IFD = [] - self._imageDataCacheIndex = [] - self._imageDataCache = [] - self._imageInfoCacheIndex = [] - self._imageInfoCache = [] - self.getImageFileDirectories(fd) - - def __makeSureFileIsOpen(self): - if not self.fd.closed: - return - if DEBUG: - print("Reopening closed file") - fileName = self.fd.name - if self._access is None: - #we do not own the file - #open in read mode - newFile = open(fileName,'rb') - else: - newFile = open(fileName, self._access) - self.fd = newFile - - def __makeSureFileIsClosed(self): - if self._access is None: - #we do not own the file - if DEBUG: - print("Not closing not owned file") - return - - if not self.fd.closed: - self.fd.close() - - def close(self): - return self.__makeSureFileIsClosed() - - def getNumberOfImages(self): - #update for the case someone has done anything? - self._updateIFD() - return len(self._IFD) - - def _updateIFD(self): - self.__makeSureFileIsOpen() - self.getImageFileDirectories() - self.__makeSureFileIsClosed() - - def getImageFileDirectories(self, fd=None): - if fd is None: - fd = self.fd - else: - self.fd = fd - st = self._structChar - fd.seek(4) - self._IFD = [] - nImages = 0 - fmt = st + 'I' - inStr = fd.read(struct.calcsize(fmt)) - if not len(inStr): - offsetToIFD = 0 - else: - offsetToIFD = struct.unpack(fmt, inStr)[0] - if DEBUG: - print("Offset to first IFD = %d" % offsetToIFD) - while offsetToIFD != 0: - self._IFD.append(offsetToIFD) - nImages += 1 - fd.seek(offsetToIFD) - fmt = st + 'H' - numberOfDirectoryEntries = struct.unpack(fmt,fd.read(struct.calcsize(fmt)))[0] - if DEBUG: - print("Number of directory entries = %d" % numberOfDirectoryEntries) - - fmt = st + 'I' - fd.seek(offsetToIFD + 2 + 12 * numberOfDirectoryEntries) - offsetToIFD = struct.unpack(fmt,fd.read(struct.calcsize(fmt)))[0] - if DEBUG: - print("Next Offset to IFD = %d" % offsetToIFD) - #offsetToIFD = 0 - if DEBUG: - print("Number of images found = %d" % nImages) - return nImages - - def _parseImageFileDirectory(self, nImage): - offsetToIFD = self._IFD[nImage] - st = self._structChar - fd = self.fd - fd.seek(offsetToIFD) - fmt = st + 'H' - numberOfDirectoryEntries = struct.unpack(fmt,fd.read(struct.calcsize(fmt)))[0] - if DEBUG: - print("Number of directory entries = %d" % numberOfDirectoryEntries) - - fmt = st + 'HHI4s' - tagIDList = [] - fieldTypeList = [] - nValuesList = [] - valueOffsetList = [] - for i in range(numberOfDirectoryEntries): - tagID, fieldType, nValues, valueOffset = struct.unpack(fmt, fd.read(12)) - tagIDList.append(tagID) - fieldTypeList.append(fieldType) - nValuesList.append(nValues) - if nValues == 1: - ftype, vfmt = FIELD_TYPE[fieldType] - if ftype not in ['ASCII', 'RATIONAL', 'SRATIONAL']: - vfmt = st + vfmt - actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] - valueOffsetList.append(actualValue) - else: - valueOffsetList.append(valueOffset) - elif (nValues < 5) and (fieldType == 2): - ftype, vfmt = FIELD_TYPE[fieldType] - vfmt = st + "%d%s" % (nValues,vfmt) - actualValue = struct.unpack(vfmt, valueOffset[0: struct.calcsize(vfmt)])[0] - valueOffsetList.append(actualValue) - else: - valueOffsetList.append(valueOffset) - if DEBUG: - if tagID in TAG_ID: - print("tagID = %s" % TAG_ID[tagID]) - else: - print("tagID = %d" % tagID) - print("fieldType = %s" % FIELD_TYPE[fieldType][0]) - print("nValues = %d" % nValues) - #if nValues == 1: - # print("valueOffset = %s" % valueOffset) - return tagIDList, fieldTypeList, nValuesList, valueOffsetList - - - - def _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList): - fd = self.fd - st = self._structChar - idx = tagIDList.index(tag) - nValues = nValuesList[idx] - output = [] - ftype, vfmt = FIELD_TYPE[fieldTypeList[idx]] - vfmt = st + "%d%s" % (nValues, vfmt) - requestedBytes = struct.calcsize(vfmt) - if nValues == 1: - output.append(valueOffsetList[idx]) - elif requestedBytes < 5: - output.append(valueOffsetList[idx]) - else: - fd.seek(struct.unpack(st+"I", valueOffsetList[idx])[0]) - output = struct.unpack(vfmt, fd.read(requestedBytes)) - return output - - def getData(self, nImage, **kw): - if nImage >= len(self._IFD): - #update prior to raise an index error error - self._updateIFD() - return self._readImage(nImage, **kw) - - def getImage(self, nImage): - return self.getData(nImage) - - def getInfo(self, nImage, **kw): - if nImage >= len(self._IFD): - #update prior to raise an index error error - self._updateIFD() - # current = self._IFD[nImage] - return self._readInfo(nImage) - - def _readInfo(self, nImage, close=True): - if nImage in self._imageInfoCacheIndex: - if DEBUG: - print("Reading info from cache") - return self._imageInfoCache[self._imageInfoCacheIndex.index(nImage)] - - #read the header - self.__makeSureFileIsOpen() - tagIDList, fieldTypeList, nValuesList, valueOffsetList = self._parseImageFileDirectory(nImage) - - #rows and columns - nColumns = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_COLUMNS)] - nRows = valueOffsetList[tagIDList.index(TAG_NUMBER_OF_ROWS)] - - #bits per sample - idx = tagIDList.index(TAG_BITS_PER_SAMPLE) - nBits = valueOffsetList[idx] - if nValuesList[idx] != 1: - #this happens with RGB and friends, nBits is not a single value - nBits = self._readIFDEntry(TAG_BITS_PER_SAMPLE, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - - - if TAG_COLORMAP in tagIDList: - idx = tagIDList.index(TAG_COLORMAP) - tmpColormap = self._readIFDEntry(TAG_COLORMAP, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - if max(tmpColormap) > 255: - tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint16) - tmpColormap = (tmpColormap/256.).astype(numpy.uint8) - else: - tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint8) - tmpColormap.shape = 3, -1 - colormap = numpy.zeros((tmpColormap.shape[-1], 3), tmpColormap.dtype) - colormap[:,:] = tmpColormap.T - tmpColormap = None - else: - colormap = None - - #sample format - if TAG_SAMPLE_FORMAT in tagIDList: - sampleFormat = valueOffsetList[tagIDList.index(TAG_SAMPLE_FORMAT)] - else: - #set to unknown - sampleFormat = SAMPLE_FORMAT_VOID - - # compression - compression = False - compression_type = 1 - if TAG_COMPRESSION in tagIDList: - compression_type = valueOffsetList[tagIDList.index(TAG_COMPRESSION)] - if compression_type == 1: - compression = False - else: - compression = True - - #photometric interpretation - interpretation = 1 - if TAG_PHOTOMETRIC_INTERPRETATION in tagIDList: - interpretation = valueOffsetList[tagIDList.index(TAG_PHOTOMETRIC_INTERPRETATION)] - else: - print("WARNING: Non standard TIFF. Photometric interpretation TAG missing") - helpString = "" - if sys.version > '2.6': - helpString = eval('b""') - - if TAG_IMAGE_DESCRIPTION in tagIDList: - imageDescription = self._readIFDEntry(TAG_IMAGE_DESCRIPTION, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - if type(imageDescription) in [type([1]), type((1,))]: - imageDescription =helpString.join(imageDescription) - else: - imageDescription = "%d/%d" % (nImage+1, len(self._IFD)) - - if sys.version < '3.0': - defaultSoftware = "Unknown Software" - else: - defaultSoftware = bytes("Unknown Software", - encoding='utf-8') - if TAG_SOFTWARE in tagIDList: - software = self._readIFDEntry(TAG_SOFTWARE, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - if type(software) in [type([1]), type((1,))]: - software =helpString.join(software) - else: - software = defaultSoftware - - if software == defaultSoftware: - try: - if sys.version < '3.0': - if imageDescription.upper().startswith("IMAGEJ"): - software = imageDescription.split("=")[0] - else: - tmpString = imageDescription.decode() - if tmpString.upper().startswith("IMAGEJ"): - software = bytes(tmpString.split("=")[0], - encoding='utf-8') - except: - pass - - if TAG_DATE in tagIDList: - date = self._readIFDEntry(TAG_DATE, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - if type(date) in [type([1]), type((1,))]: - date =helpString.join(date) - else: - date = "Unknown Date" - - stripOffsets = self._readIFDEntry(TAG_STRIP_OFFSETS, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - if TAG_ROWS_PER_STRIP in tagIDList: - rowsPerStrip = self._readIFDEntry(TAG_ROWS_PER_STRIP, - tagIDList, fieldTypeList, nValuesList, valueOffsetList)[0] - else: - rowsPerStrip = nRows - print("WARNING: Non standard TIFF. Rows per strip TAG missing") - - if TAG_STRIP_BYTE_COUNTS in tagIDList: - stripByteCounts = self._readIFDEntry(TAG_STRIP_BYTE_COUNTS, - tagIDList, fieldTypeList, nValuesList, valueOffsetList) - else: - print("WARNING: Non standard TIFF. Strip byte counts TAG missing") - if hasattr(nBits, 'index'): - expectedSum = 0 - for n in nBits: - expectedSum += int(nRows * nColumns * n / 8) - else: - expectedSum = int(nRows * nColumns * nBits / 8) - stripByteCounts = [expectedSum] - - if close: - self.__makeSureFileIsClosed() - - if self._forceMonoOutput and (interpretation > 1): - #color image but asked monochrome output - nBits = 32 - colormap = None - sampleFormat = SAMPLE_FORMAT_FLOAT - interpretation = 1 - #we cannot rely on any cache in this case - useInfoCache = False - if DEBUG: - print("FORCED MONO") - else: - useInfoCache = True - - info = {} - info["nRows"] = nRows - info["nColumns"] = nColumns - info["nBits"] = nBits - info["compression"] = compression - info["compression_type"] = compression_type - info["imageDescription"] = imageDescription - info["stripOffsets"] = stripOffsets #This contains the file offsets to the data positions - info["rowsPerStrip"] = rowsPerStrip - info["stripByteCounts"] = stripByteCounts #bytes in strip since I do not support compression - info["software"] = software - info["date"] = date - info["colormap"] = colormap - info["sampleFormat"] = sampleFormat - info["photometricInterpretation"] = interpretation - infoDict = {} - if sys.version < '3.0': - testString = 'PyMca' - else: - testString = eval('b"PyMca"') - if software.startswith(testString): - #str to make sure python 2.x sees it as string and not unicode - if sys.version < '3.0': - descriptionString = imageDescription - else: - descriptionString = str(imageDescription.decode()) - #interpret the image description in terms of supplied - #information at writing time - items = descriptionString.split('=') - for i in range(int(len(items)/2)): - key = "%s" % items[i*2] - #get rid of the \n at the end of the value - value = "%s" % items[i*2+1][:-1] - infoDict[key] = value - info['info'] = infoDict - - if (self._maxImageCacheLength > 0) and useInfoCache: - self._imageInfoCacheIndex.insert(0,nImage) - self._imageInfoCache.insert(0, info) - if len(self._imageInfoCacheIndex) > self._maxImageCacheLength: - self._imageInfoCacheIndex = self._imageInfoCacheIndex[:self._maxImageCacheLength] - self._imageInfoCache = self._imageInfoCache[:self._maxImageCacheLength] - return info - - def _readImage(self, nImage, **kw): - if DEBUG: - print("Reading image %d" % nImage) - if 'close' in kw: - close = kw['close'] - else: - close = True - rowMin = kw.get('rowMin', None) - rowMax = kw.get('rowMax', None) - if nImage in self._imageDataCacheIndex: - if DEBUG: - print("Reading image data from cache") - return self._imageDataCache[self._imageDataCacheIndex.index(nImage)] - - self.__makeSureFileIsOpen() - if self._forceMonoOutput: - oldMono = True - else: - oldMono = False - try: - self._forceMonoOutput = False - info = self._readInfo(nImage, close=False) - self._forceMonoOutput = oldMono - except: - self._forceMonoOutput = oldMono - raise - compression = info['compression'] - compression_type = info['compression_type'] - if compression: - if compression_type != 32773: - raise IOError("Compressed TIFF images not supported except packbits") - else: - #PackBits compression - if DEBUG: - print("Using PackBits compression") - - interpretation = info["photometricInterpretation"] - if interpretation == 2: - #RGB - pass - #raise IOError("RGB Image. Only grayscale images supported") - elif interpretation == 3: - #Palette Color Image - pass - #raise IOError("Palette-color Image. Only grayscale images supported") - elif interpretation > 2: - #Palette Color Image - raise IOError("Only grayscale images supported") - - nRows = info["nRows"] - nColumns = info["nColumns"] - nBits = info["nBits"] - colormap = info["colormap"] - sampleFormat = info["sampleFormat"] - - if rowMin is None: - rowMin = 0 - - if rowMax is None: - rowMax = nRows - 1 - - if rowMin < 0: - rowMin = nRows - rowMin - - if rowMax < 0: - rowMax = nRows - rowMax - - if rowMax < rowMin: - txt = "Max Row smaller than Min Row. Reverse selection not supported" - raise NotImplementedError(txt) - - if rowMin >= nRows: - raise IndexError("Image only has %d rows" % nRows) - - if rowMax >= nRows: - raise IndexError("Image only has %d rows" % nRows) - - if sampleFormat == SAMPLE_FORMAT_FLOAT: - if nBits == 32: - dtype = numpy.float32 - elif nBits == 64: - dtype = numpy.float64 - else: - raise ValueError("Unsupported number of bits for a float: %d" % nBits) - elif sampleFormat in [SAMPLE_FORMAT_UINT, SAMPLE_FORMAT_VOID]: - if nBits in [8, (8, 8, 8), [8, 8, 8]]: - dtype = numpy.uint8 - elif nBits in [16, (16, 16, 16), [16, 16, 16]]: - dtype = numpy.uint16 - elif nBits in [32, (32, 32, 32), [32, 32, 32]]: - dtype = numpy.uint32 - elif nBits in [64, (64, 64, 64), [64, 64, 64]]: - dtype = numpy.uint64 - else: - raise ValueError("Unsupported number of bits for unsigned int: %s" % (nBits,)) - elif sampleFormat == SAMPLE_FORMAT_INT: - if nBits in [8, (8, 8, 8), [8, 8, 8]]: - dtype = numpy.int8 - elif nBits in [16, (16, 16, 16), [16, 16, 16]]: - dtype = numpy.int16 - elif nBits in [32, (32, 32, 32), [32, 32, 32]]: - dtype = numpy.int32 - elif nBits in [64, (64, 64, 64), [64, 64, 64]]: - dtype = numpy.int64 - else: - raise ValueError("Unsupported number of bits for signed int: %s" % (nBits,)) - else: - raise ValueError("Unsupported combination. Bits = %s Format = %d" % (nBits, sampleFormat)) - if hasattr(nBits, 'index'): - image = numpy.zeros((nRows, nColumns, len(nBits)), dtype=dtype) - elif colormap is not None: - #should I use colormap dtype? - image = numpy.zeros((nRows, nColumns, 3), dtype=dtype) - else: - image = numpy.zeros((nRows, nColumns), dtype=dtype) - - fd = self.fd - st = self._structChar - stripOffsets = info["stripOffsets"] #This contains the file offsets to the data positions - rowsPerStrip = info["rowsPerStrip"] - stripByteCounts = info["stripByteCounts"] #bytes in strip since I do not support compression - - rowStart = 0 - if len(stripOffsets) == 1: - bytesPerRow = int(stripByteCounts[0]/rowsPerStrip) - if nRows == rowsPerStrip: - actualBytesPerRow = int(image.nbytes/nRows) - if actualBytesPerRow != bytesPerRow: - print("Warning: Bogus StripByteCounts information") - bytesPerRow = actualBytesPerRow - fd.seek(stripOffsets[0] + rowMin * bytesPerRow) - nBytes = (rowMax-rowMin+1) * bytesPerRow - if self._swap: - readout = numpy.copy(numpy.frombuffer(fd.read(nBytes), dtype)).byteswap() - else: - readout = numpy.copy(numpy.frombuffer(fd.read(nBytes), dtype)) - if hasattr(nBits, 'index'): - readout.shape = -1, nColumns, len(nBits) - elif info['colormap'] is not None: - readout = colormap[readout] - else: - readout.shape = -1, nColumns - image[rowMin:rowMax+1, :] = readout - else: - for i in range(len(stripOffsets)): - #the amount of rows - nRowsToRead = rowsPerStrip - rowEnd = int(min(rowStart+nRowsToRead, nRows)) - if rowEnd < rowMin: - rowStart += nRowsToRead - continue - if (rowStart > rowMax): - break - #we are in position - fd.seek(stripOffsets[i]) - #the amount of bytes to read - nBytes = stripByteCounts[i] - if compression_type == 32773: - try: - bufferBytes = bytes() - except: - #python 2.5 ... - bufferBytes = "" - #packBits - readBytes = 0 - #intermediate buffer - tmpBuffer = fd.read(nBytes) - while readBytes < nBytes: - n = struct.unpack('b', tmpBuffer[readBytes:(readBytes+1)])[0] - readBytes += 1 - if n >= 0: - #should I prevent reading more than the - #length of the chain? Let's python raise - #the exception... - bufferBytes += tmpBuffer[readBytes:\ - readBytes+(n+1)] - readBytes += (n+1) - elif n > -128: - bufferBytes += (-n+1) * tmpBuffer[readBytes:(readBytes+1)] - readBytes += 1 - else: - #if read -128 ignore the byte - continue - if self._swap: - readout = numpy.copy(numpy.frombuffer(bufferBytes, dtype)).byteswap() - else: - readout = numpy.copy(numpy.frombuffer(bufferBytes, dtype)) - if hasattr(nBits, 'index'): - readout.shape = -1, nColumns, len(nBits) - elif info['colormap'] is not None: - readout = colormap[readout] - readout.shape = -1, nColumns, 3 - else: - readout.shape = -1, nColumns - image[rowStart:rowEnd, :] = readout - else: - if 1: - #use numpy - if self._swap: - readout = numpy.copy(numpy.frombuffer(fd.read(nBytes), dtype)).byteswap() - else: - readout = numpy.copy(numpy.frombuffer(fd.read(nBytes), dtype)) - if hasattr(nBits, 'index'): - readout.shape = -1, nColumns, len(nBits) - elif colormap is not None: - readout = colormap[readout] - readout.shape = -1, nColumns, 3 - else: - readout.shape = -1, nColumns - image[rowStart:rowEnd, :] = readout - else: - #using struct - readout = numpy.array(struct.unpack(st+"%df" % int(nBytes/4), fd.read(nBytes)), - dtype=dtype) - if hasattr(nBits, 'index'): - readout.shape = -1, nColumns, len(nBits) - elif colormap is not None: - readout = colormap[readout] - readout.shape = -1, nColumns, 3 - else: - readout.shape = -1, nColumns - image[rowStart:rowEnd, :] = readout - rowStart += nRowsToRead - if close: - self.__makeSureFileIsClosed() - - if len(image.shape) == 3: - #color image - if self._forceMonoOutput: - #color image, convert to monochrome - image = (image[:,:,0] * 0.114 +\ - image[:,:,1] * 0.587 +\ - image[:,:,2] * 0.299).astype(numpy.float32) - - if (rowMin == 0) and (rowMax == (nRows-1)): - self._imageDataCacheIndex.insert(0,nImage) - self._imageDataCache.insert(0, image) - if len(self._imageDataCacheIndex) > self._maxImageCacheLength: - self._imageDataCacheIndex = self._imageDataCacheIndex[:self._maxImageCacheLength] - self._imageDataCache = self._imageDataCache[:self._maxImageCacheLength] - - return image - - def writeImage(self, image0, info=None, software=None, date=None): - if software is None: - software = 'PyMca.TiffIO' - #if date is None: - # date = time.ctime() - - self.__makeSureFileIsOpen() - fd = self.fd - #prior to do anything, perform some tests - if not len(image0.shape): - raise ValueError("Empty image") - if len(image0.shape) == 1: - #get a different view - image = image0[:] - image.shape = 1, -1 - else: - image = image0 - - if image.dtype == numpy.float64: - image = image.astype(numpy.float32) - fd.seek(0) - mode = fd.mode - name = fd.name - if 'w' in mode: - #we have to overwrite the file - self.__makeSureFileIsClosed() - fd = None - if os.path.exists(name): - os.remove(name) - fd = open(name, mode='wb+') - self._initEmptyFile(fd) - self.fd = fd - - #read the file size - self.__makeSureFileIsOpen() - fd = self.fd - fd.seek(0, os.SEEK_END) - endOfFile = fd.tell() - if fd.tell() == 0: - self._initEmptyFile(fd) - fd.seek(0, os.SEEK_END) - endOfFile = fd.tell() - - #init internal variables - self._initInternalVariables(fd) - st = self._structChar - - #get the image file directories - nImages = self.getImageFileDirectories() - if DEBUG: - print("File contains %d images" % nImages) - if nImages == 0: - fd.seek(4) - fmt = st + 'I' - fd.write(struct.pack(fmt, endOfFile)) - else: - fd.seek(self._IFD[-1]) - fmt = st + 'H' - numberOfDirectoryEntries = struct.unpack(fmt,fd.read(struct.calcsize(fmt)))[0] - fmt = st + 'I' - pos = self._IFD[-1] + 2 + 12 * numberOfDirectoryEntries - fd.seek(pos) - fmt = st + 'I' - fd.write(struct.pack(fmt, endOfFile)) - fd.flush() - - #and we can write at the end of the file, find out the file length - fd.seek(0, os.SEEK_END) - - #get the description information from the input information - if info is None: - description = info - else: - description = "%s" % "" - for key in info.keys(): - description += "%s=%s\n" % (key, info[key]) - - #get the image file directory - outputIFD = self._getOutputIFD(image, description=description, - software=software, - date=date) - - #write the new IFD - fd.write(outputIFD) - - #write the image - if self._swap: - fd.write(image.byteswap().tobytes()) - else: - fd.write(image.tobytes()) - - fd.flush() - self.fd=fd - self.__makeSureFileIsClosed() - - def _initEmptyFile(self, fd=None): - if fd is None: - fd = self.fd - if sys.byteorder == "little": - order = "II" - #intel, little endian - fileOrder = "little" - self._structChar = '<' - else: - order = "MM" - #motorola, high endian - fileOrder = "big" - self._structChar = '>' - st = self._structChar - if fileOrder == sys.byteorder: - self._swap = False - else: - self._swap = True - fd.seek(0) - if sys.version < '3.0': - fd.write(struct.pack(st+'2s', order)) - fd.write(struct.pack(st+'H', 42)) - fd.write(struct.pack(st+'I', 0)) - else: - fd.write(struct.pack(st+'2s', bytes(order,'utf-8'))) - fd.write(struct.pack(st+'H', 42)) - fd.write(struct.pack(st+'I', 0)) - fd.flush() - - def _getOutputIFD(self, image, description=None, software=None, date=None): - #the tags have to be in order - #the very minimum is - #256:"NumberOfColumns", # S or L ImageWidth - #257:"NumberOfRows", # S or L ImageHeight - #258:"BitsPerSample", # S Number of bits per component - #259:"Compression", # SHORT (1 - NoCompression, ... - #262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color - #270:"ImageDescription", # ASCII - #273:"StripOffsets", # S or L, for each strip, the byte offset of the strip - #277:"SamplesPerPixel", # SHORT (>=3) only for RGB images - #278:"RowsPerStrip", # S or L, number of rows in each back may be not for the last - #279:"StripByteCounts", # S or L, The number of bytes in the strip AFTER any compression - #305:"Software", # ASCII - #306:"Date", # ASCII - #339:"SampleFormat", # SHORT Interpretation of data in each pixel - - nDirectoryEntries = 9 - imageDescription = None - if description is not None: - descriptionLength = len(description) - while descriptionLength < 4: - description = description + " " - descriptionLength = len(description) - if sys.version >= '3.0': - description = bytes(description, 'utf-8') - elif type(description) != type(""): - try: - description = description.decode('utf-8') - except UnicodeDecodeError: - try: - description = description.decode('latin-1') - except UnicodeDecodeError: - description = "%s" % description - if sys.version > '2.6': - description=description.encode('utf-8', errors="ignore") - description = "%s" % description - descriptionLength = len(description) - imageDescription = struct.pack("%ds" % descriptionLength, description) - nDirectoryEntries += 1 - - #software - if software is not None: - softwareLength = len(software) - while softwareLength < 4: - software = software + " " - softwareLength = len(software) - if sys.version >= '3.0': - software = bytes(software, 'utf-8') - softwarePackedString = struct.pack("%ds" % softwareLength, software) - nDirectoryEntries += 1 - else: - softwareLength = 0 - - if date is not None: - dateLength = len(date) - if sys.version >= '3.0': - date = bytes(date, 'utf-8') - datePackedString = struct.pack("%ds" % dateLength, date) - dateLength = len(datePackedString) - nDirectoryEntries += 1 - else: - dateLength = 0 - - if len(image.shape) == 2: - nRows, nColumns = image.shape - nChannels = 1 - elif len(image.shape) == 3: - nRows, nColumns, nChannels = image.shape - else: - raise RuntimeError("Image does not have the right shape") - dtype = image.dtype - bitsPerSample = int(dtype.str[-1]) * 8 - - #only uncompressed data - compression = 1 - - #interpretation, black is zero - if nChannels == 1: - interpretation = 1 - bitsPerSampleLength = 0 - elif nChannels == 3: - interpretation = 2 - bitsPerSampleLength = 3 * 2 # To store 3 shorts - nDirectoryEntries += 1 # For SamplesPerPixel - else: - raise RuntimeError( - "Image with %d color channel(s) not supported" % nChannels) - - #image description - if imageDescription is not None: - descriptionLength = len(imageDescription) - else: - descriptionLength = 0 - - #strip offsets - #we are putting them after the directory and the directory is - #at the end of the file - self.fd.seek(0, os.SEEK_END) - endOfFile = self.fd.tell() - if endOfFile == 0: - #empty file - endOfFile = 8 - - #rows per strip - if ALLOW_MULTIPLE_STRIPS: - #try to segment the image in several pieces - if not (nRows % 4): - rowsPerStrip = int(nRows/4) - elif not (nRows % 10): - rowsPerStrip = int(nRows/10) - elif not (nRows % 8): - rowsPerStrip = int(nRows/8) - elif not (nRows % 4): - rowsPerStrip = int(nRows/4) - elif not (nRows % 2): - rowsPerStrip = int(nRows/2) - else: - rowsPerStrip = nRows - else: - rowsPerStrip = nRows - - #stripByteCounts - stripByteCounts = int(nColumns * rowsPerStrip * - bitsPerSample * nChannels / 8) - - if descriptionLength > 4: - stripOffsets0 = endOfFile + dateLength + descriptionLength +\ - 2 + 12 * nDirectoryEntries + 4 - else: - stripOffsets0 = endOfFile + dateLength + \ - 2 + 12 * nDirectoryEntries + 4 - - if softwareLength > 4: - stripOffsets0 += softwareLength - - stripOffsets0 += bitsPerSampleLength - - stripOffsets = [stripOffsets0] - stripOffsetsLength = 0 - stripOffsetsString = None - - st = self._structChar - - if rowsPerStrip != nRows: - nStripOffsets = int(nRows/rowsPerStrip) - fmt = st + 'I' - stripOffsetsLength = struct.calcsize(fmt) * nStripOffsets - stripOffsets0 += stripOffsetsLength - #the length for the stripByteCounts will be the same - stripOffsets0 += stripOffsetsLength - stripOffsets = [] - for i in range(nStripOffsets): - value = stripOffsets0 + i * stripByteCounts - stripOffsets.append(value) - if i == 0: - stripOffsetsString = struct.pack(fmt, value) - stripByteCountsString = struct.pack(fmt, stripByteCounts) - else: - stripOffsetsString += struct.pack(fmt, value) - stripByteCountsString += struct.pack(fmt, stripByteCounts) - - if DEBUG: - print("IMAGE WILL START AT %d" % stripOffsets[0]) - - #sample format - if dtype in [numpy.float32, numpy.float64] or\ - dtype.str[-2] == 'f': - sampleFormat = SAMPLE_FORMAT_FLOAT - elif dtype in [numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64]: - sampleFormat = SAMPLE_FORMAT_UINT - elif dtype in [numpy.int8, numpy.int16, numpy.int32, numpy.int64]: - sampleFormat = SAMPLE_FORMAT_INT - else: - raise ValueError("Unsupported data type %s" % dtype) - - info = {} - info["nColumns"] = nColumns - info["nRows"] = nRows - info["nBits"] = bitsPerSample - info["compression"] = compression - info["photometricInterpretation"] = interpretation - info["stripOffsets"] = stripOffsets - if interpretation == 2: - info["samplesPerPixel"] = 3 # No support for extra samples - info["rowsPerStrip"] = rowsPerStrip - info["stripByteCounts"] = stripByteCounts - info["date"] = date - info["sampleFormat"] = sampleFormat - - outputIFD = "" - if sys.version > '2.6': - outputIFD = eval('b""') - - fmt = st + "H" - outputIFD += struct.pack(fmt, nDirectoryEntries) - - fmt = st + "HHII" - outputIFD += struct.pack(fmt, TAG_NUMBER_OF_COLUMNS, - FIELD_TYPE_OUT['I'], - 1, - info["nColumns"]) - outputIFD += struct.pack(fmt, TAG_NUMBER_OF_ROWS, - FIELD_TYPE_OUT['I'], - 1, - info["nRows"]) - - if info["photometricInterpretation"] == 1: - fmt = st + 'HHIHH' - outputIFD += struct.pack(fmt, TAG_BITS_PER_SAMPLE, - FIELD_TYPE_OUT['H'], - 1, - info["nBits"], 0) - elif info["photometricInterpretation"] == 2: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_BITS_PER_SAMPLE, - FIELD_TYPE_OUT['H'], - 3, - info["stripOffsets"][0] - \ - 2 * stripOffsetsLength - \ - descriptionLength - \ - dateLength - \ - softwareLength - \ - bitsPerSampleLength) - else: - raise RuntimeError("Unsupported photometric interpretation") - - fmt = st + 'HHIHH' - outputIFD += struct.pack(fmt, TAG_COMPRESSION, - FIELD_TYPE_OUT['H'], - 1, - info["compression"],0) - fmt = st + 'HHIHH' - outputIFD += struct.pack(fmt, TAG_PHOTOMETRIC_INTERPRETATION, - FIELD_TYPE_OUT['H'], - 1, - info["photometricInterpretation"],0) - - if imageDescription is not None: - descriptionLength = len(imageDescription) - if descriptionLength > 4: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, - FIELD_TYPE_OUT['s'], - descriptionLength, - info["stripOffsets"][0]-\ - 2*stripOffsetsLength-\ - descriptionLength) - else: - #it has to have length 4 - fmt = st + 'HHI%ds' % descriptionLength - outputIFD += struct.pack(fmt, TAG_IMAGE_DESCRIPTION, - FIELD_TYPE_OUT['s'], - descriptionLength, - description) - - if len(stripOffsets) == 1: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, - FIELD_TYPE_OUT['I'], - 1, - info["stripOffsets"][0]) - else: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_STRIP_OFFSETS, - FIELD_TYPE_OUT['I'], - len(stripOffsets), - info["stripOffsets"][0]-2*stripOffsetsLength) - - if info["photometricInterpretation"] == 2: - fmt = st + 'HHIHH' - outputIFD += struct.pack(fmt, TAG_SAMPLES_PER_PIXEL, - FIELD_TYPE_OUT['H'], - 1, - info["samplesPerPixel"], 0) - - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_ROWS_PER_STRIP, - FIELD_TYPE_OUT['I'], - 1, - info["rowsPerStrip"]) - - if len(stripOffsets) == 1: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, - FIELD_TYPE_OUT['I'], - 1, - info["stripByteCounts"]) - else: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_STRIP_BYTE_COUNTS, - FIELD_TYPE_OUT['I'], - len(stripOffsets), - info["stripOffsets"][0]-stripOffsetsLength) - - if software is not None: - if softwareLength > 4: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_SOFTWARE, - FIELD_TYPE_OUT['s'], - softwareLength, - info["stripOffsets"][0]-\ - 2*stripOffsetsLength-\ - descriptionLength-softwareLength-dateLength) - else: - #it has to have length 4 - fmt = st + 'HHI%ds' % softwareLength - outputIFD += struct.pack(fmt, TAG_SOFTWARE, - FIELD_TYPE_OUT['s'], - softwareLength, - softwarePackedString) - - if date is not None: - fmt = st + 'HHII' - outputIFD += struct.pack(fmt, TAG_DATE, - FIELD_TYPE_OUT['s'], - dateLength, - info["stripOffsets"][0]-\ - 2*stripOffsetsLength-\ - descriptionLength-dateLength) - - fmt = st + 'HHIHH' - outputIFD += struct.pack(fmt, TAG_SAMPLE_FORMAT, - FIELD_TYPE_OUT['H'], - 1, - info["sampleFormat"],0) - fmt = st + 'I' - outputIFD += struct.pack(fmt, 0) - - if info["photometricInterpretation"] == 2: - outputIFD += struct.pack('HHH', info["nBits"], - info["nBits"], info["nBits"]) - - if softwareLength > 4: - outputIFD += softwarePackedString - - if date is not None: - outputIFD += datePackedString - - if imageDescription is not None: - if descriptionLength > 4: - outputIFD += imageDescription - - if stripOffsetsString is not None: - outputIFD += stripOffsetsString - outputIFD += stripByteCountsString - - return outputIFD - - -if __name__ == "__main__": - filename = sys.argv[1] - dtype = numpy.uint16 - if not os.path.exists(filename): - print("Testing file creation") - tif = TiffIO(filename, mode = 'wb+') - data = numpy.arange(10000).astype(dtype) - data.shape = 100, 100 - tif.writeImage(data, info={'Title':'1st'}) - tif = None - if os.path.exists(filename): - print("Testing image appending") - tif = TiffIO(filename, mode = 'rb+') - tif.writeImage((data*2).astype(dtype), info={'Title':'2nd'}) - tif = None - tif = TiffIO(filename) - print("Number of images = %d" % tif.getNumberOfImages()) - for i in range(tif.getNumberOfImages()): - info = tif.getInfo(i) - for key in info: - if key not in ["colormap"]: - print("%s = %s" % (key, info[key])) - elif info['colormap'] is not None: - print("RED %s = %s" % (key, info[key][0:10, 0])) - print("GREEN %s = %s" % (key, info[key][0:10, 1])) - print("BLUE %s = %s" % (key, info[key][0:10, 2])) - data = tif.getImage(i)[0, 0:10] - print("data [0, 0:10] = ", data) - diff --git a/silx/third_party/__init__.py b/silx/third_party/__init__.py deleted file mode 100644 index 156563c..0000000 --- a/silx/third_party/__init__.py +++ /dev/null @@ -1,33 +0,0 @@ -# coding: utf-8 -# /*########################################################################## -# -# Copyright (c) 2015-2018 European Synchrotron Radiation Facility -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# ###########################################################################*/ -"""This package embeds a few dependency of silx. - -This is meant for internal use. -""" - - -__authors__ = ["Jérôme Kieffer"] -__license__ = "MIT" -__date__ = "09/10/2015" diff --git a/silx/third_party/scipy_spatial.py b/silx/third_party/scipy_spatial.py deleted file mode 100644 index 9885154..0000000 --- a/silx/third_party/scipy_spatial.py +++ /dev/null @@ -1,51 +0,0 @@ -# coding: utf-8 -# /*########################################################################## -# -# Copyright (c) 2017 European Synchrotron Radiation Facility -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# ###########################################################################*/ -"""Wrapper module for `scipy.spatial.Delaunay` class. - -Uses a local copy of `scipy.spatial.Delaunay` if available, -else it loads it from `scipy`. - -It should be used like that: - -.. code-block:: - - from silx.third_party.scipy_spatial import Delaunay - -""" - -from __future__ import absolute_import - -__authors__ = ["T. Vincent"] -__license__ = "MIT" -__date__ = "07/11/2017" - -try: - # try to import silx local copy of Delaunay - from ._local.scipy_spatial import Delaunay # noqa -except ImportError: - # else import it from the python path - from scipy.spatial import Delaunay # noqa - -__all__ = ['Delaunay'] diff --git a/silx/third_party/setup.py b/silx/third_party/setup.py deleted file mode 100644 index dd3d302..0000000 --- a/silx/third_party/setup.py +++ /dev/null @@ -1,49 +0,0 @@ -# coding: ascii -# -# JK: Numpy.distutils which imports this does not handle utf-8 in version<1.12 -# -# /*########################################################################## -# -# Copyright (c) 2016-2018 European Synchrotron Radiation Facility -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# ###########################################################################*/ - -__authors__ = ["Valentin Valls"] -__license__ = "MIT" -__date__ = "23/04/2018" - -import os -from numpy.distutils.misc_util import Configuration - - -def configuration(parent_package='', top_path=None): - config = Configuration('third_party', parent_package, top_path) - # includes _local only if it is available - local_path = os.path.join(top_path, "silx", "third_party", "_local") - if os.path.exists(local_path): - config.add_subpackage('_local') - config.add_subpackage('_local.scipy_spatial') - return config - - -if __name__ == "__main__": - from numpy.distutils.core import setup - setup(configuration=configuration) |