path: root/silx/third_party/EdfFile.py

# /*##########################################################################
#
# Copyright (c) 2004-2018 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.fromstring(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.fromstring(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.fromstring(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.fromstring(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.fromstring(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.fromstring(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.fromstring(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.fromstring(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()).tostring())
        else:
            self.File.write(Data.tostring())

    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"])