New upstream version 5.3.2+dfsg

6 files changed, 141 insertions, 71 deletions

diff --git a/PyMca5/PyMcaIO/EdfFile.py b/PyMca5/PyMcaIO/EdfFile.py
index 418771f..481ca6e 100644
--- a/PyMca5/PyMcaIO/EdfFile.py
+++ b/PyMca5/PyMcaIO/EdfFile.py
@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
+# 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.
@@ -443,7 +443,7 @@ class  EdfFile(object):
             self.Images[Index].DataType = 'UnsignedShort'
             try:
                 self.__data = numpy.reshape(
-                    numpy.fromstring(binary, numpy.uint16),
+                    numpy.array(numpy.frombuffer(binary, numpy.uint16)),
                     (self.Images[Index].Dim2, self.Images[Index].Dim1))
             except ValueError:
                 raise IOError('Size spec in ADSC-header does not match ' + \
@@ -636,14 +636,14 @@ class  EdfFile(object):
                     sizeToRead = self.Images[Index].Dim1 * \
                                  self.Images[Index].Dim2 * \
                                  self.Images[Index].Dim3 * datasize
-                    Data = numpy.fromstring(self.File.read(sizeToRead),
-                                datatype)
+                    Data = numpy.array(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:
                     sizeToRead = self.Images[Index].Dim1 * \
                                  self.Images[Index].Dim2 * datasize
-                    Data = numpy.fromstring(self.File.read(sizeToRead),
-                                datatype)
+                    Data = numpy.array(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
@@ -654,8 +654,8 @@ class  EdfFile(object):
                     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)
+                    Data = numpy.array(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])]
@@ -664,9 +664,9 @@ class  EdfFile(object):
             return data[Pos[1]:(Pos[1] + Size[1]),
                                Pos[0]:(Pos[0] + Size[0])]
         elif fastedf and CAN_USE_FASTEDF:
-            type = self.__GetDefaultNumpyType__(self.Images[Index].DataType, index=Index)
-            size_pixel = self.__GetSizeNumpyType__(type)
-            Data = numpy.array([], type)
+            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 == None: Pos = (0,)
                 if Size == None: Size = (0,)
@@ -674,7 +674,7 @@ class  EdfFile(object):
                 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)
+                Data = numpy.array(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_))
             elif self.Images[Index].NumDim == 2:
                 if Pos == None: Pos = (0, 0)
                 if Size == None: Size = (0, 0)
@@ -682,7 +682,7 @@ class  EdfFile(object):
                 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]
-                Data = numpy.zeros([Size[1], Size[0]], type)
+                Data = numpy.zeros([Size[1], Size[0]], type_)
                 self.File.seek((((Pos[1] * sizex) + Pos[0]) * size_pixel) + self.Images[Index].DataPosition, 0)
                 extended_fread(Data, Size[0] * size_pixel , numpy.array([Size[1]]),
                                numpy.array([sizex * size_pixel]) , self.File)
@@ -695,7 +695,7 @@ class  EdfFile(object):
                 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]
-                Data = numpy.zeros([Size[2], Size[1], Size[0]], type)
+                Data = numpy.zeros([Size[2], Size[1], Size[0]], type_)
                 self.File.seek(((((Pos[2] * sizey + Pos[1]) * sizex) + Pos[0]) * size_pixel) + self.Images[Index].DataPosition, 0)
                 extended_fread(Data, Size[0] * size_pixel , numpy.array([Size[2], Size[1]]),
                         numpy.array([ sizey * sizex * size_pixel , sizex * size_pixel]) , self.File)
@@ -703,9 +703,9 @@ class  EdfFile(object):
         else:
             if fastedf:
                 print("I could not use fast routines")
-            type = self.__GetDefaultNumpyType__(self.Images[Index].DataType, index=Index)
-            size_pixel = self.__GetSizeNumpyType__(type)
-            Data = numpy.array([], type)
+            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 == None: Pos = (0,)
                 if Size == None: Size = (0,)
@@ -713,7 +713,7 @@ class  EdfFile(object):
                 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)
+                Data = numpy.array(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_))
             elif self.Images[Index].NumDim == 2:
                 if Pos == None: Pos = (0, 0)
                 if Size == None: Size = (0, 0)
@@ -723,11 +723,11 @@ class  EdfFile(object):
                 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)
+                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)
+                    line = numpy.array(numpy.frombuffer(self.File.read(Size[0] * size_pixel), type_))
                     Data[dataindex, :] = line[:]
                     #Data=numpy.concatenate((Data,line))
                     dataindex += 1
@@ -745,7 +745,7 @@ class  EdfFile(object):
                 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)
+                        line = numpy.array(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]))
 
@@ -776,9 +776,10 @@ class  EdfFile(object):
                 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))
+        Data = numpy.array(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")
@@ -931,7 +932,7 @@ class  EdfFile(object):
         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 = (((len(StrHeader) + 1) // HEADER_BLOCK_SIZE) + 1) * HEADER_BLOCK_SIZE - 2
         newsize = int(newsize)
         StrHeader = StrHeader.ljust(newsize)
         StrHeader = StrHeader + "}\n"
diff --git a/PyMca5/PyMcaIO/HDF5Stack1D.py b/PyMca5/PyMcaIO/HDF5Stack1D.py
index 2c41858..041bf1e 100644
--- a/PyMca5/PyMcaIO/HDF5Stack1D.py
+++ b/PyMca5/PyMcaIO/HDF5Stack1D.py
@@ -256,7 +256,10 @@ class HDF5Stack1D(DataObject.DataObject):
             if self.__dtype in [numpy.int16, numpy.uint16]:
                 self.__dtype = numpy.float32
             elif self.__dtype in [numpy.int32, numpy.uint32]:
-                self.__dtype = numpy.float64
+                if mSelection:
+                    self.__dtype = numpy.float32
+                else:
+                    self.__dtype = numpy.float64
             elif self.__dtype not in [numpy.float16, numpy.float32,
                                       numpy.float64]:
                 # Some datasets form CLS (origin APS?) arrive as data format
@@ -266,7 +269,10 @@ class HDF5Stack1D(DataObject.DataObject):
                 if ("%s" % self.__dtype).endswith("2"):
                     self.__dtype = numpy.float32
                 else:
-                    self.__dtype = numpy.float64
+                    if mSelection:
+                        self.__dtype = numpy.float32
+                    else:
+                        self.__dtype = numpy.float64
 
         # figure out the shape of the stack
         shape = yDataset.shape
@@ -289,9 +295,14 @@ class HDF5Stack1D(DataObject.DataObject):
                 bytefactor = 8
 
             neededMegaBytes = nFiles * dim0 * dim1 * (mcaDim * bytefactor/(1024*1024.))
-            physicalMemory = PhysicalMemory.getPhysicalMemoryOrNone()
+            physicalMemory = None
+            if hasattr(PhysicalMemory, "getAvailablePhysicalMemoryOrNone"):
+                physicalMemory = PhysicalMemory.getAvailablePhysicalMemoryOrNone()
+            if not physicalMemory:
+                physicalMemory = PhysicalMemory.getPhysicalMemoryOrNone()
             if physicalMemory is None:
-                # 5 Gigabytes should be a good compromise
+                # 6 Gigabytes of available memory
+                # should be a good compromise in 2018
                 physicalMemory = 6000
             else:
                 physicalMemory /= (1024*1024.)
@@ -300,6 +311,7 @@ class HDF5Stack1D(DataObject.DataObject):
                 if self.__dtype0 is None:
                     if (bytefactor == 8) and (neededMegaBytes < (2*physicalMemory)):
                         # try reading as float32
+                        print("Forcing the use of float32 data")
                         self.__dtype = numpy.float32
                     else:
                         raise MemoryError("Force dynamic loading")
@@ -317,6 +329,8 @@ class HDF5Stack1D(DataObject.DataObject):
             # some versions report ValueError instead of MemoryError
             if (nFiles == 1) and (len(shape) == 3):
                 print("Attempting dynamic loading")
+                if mSelection is not None:
+                    print("Ignoring monitor")
                 self.data = yDataset
                 if mSelection is not None:
                     mdtype = tmpHdf[mpath].dtype
diff --git a/PyMca5/PyMcaIO/MarCCD.py b/PyMca5/PyMcaIO/MarCCD.py
index fc37031..f2d0c8e 100644
--- a/PyMca5/PyMcaIO/MarCCD.py
+++ b/PyMca5/PyMcaIO/MarCCD.py
@@ -64,11 +64,11 @@ class MarCCD(object):
         depth  = info["depth"]
         fd.seek(4096)
         if depth == 1:
-            data = numpy.fromstring(fd.read(nbytes), numpy.uint8)
+            data = numpy.array(numpy.frombuffer(fd.read(nbytes), numpy.uint8))
         elif depth == 2:
-            data = numpy.fromstring(fd.read(nbytes), numpy.uint16)
+            data = numpy.array(numpy.frombuffer(fd.read(nbytes), numpy.uint16))
         elif depth == 4:
-            data = numpy.fromstring(fd.read(nbytes), numpy.uint32)
+            data = numpy.array(numpy.frombuffer(fd.read(nbytes), numpy.uint32))
         if swap:
             data = data.byteswap()
         data.shape = info["nfast"], info["nslow"]
@@ -155,7 +155,7 @@ class MccdHeader(object):
         if 0:
             self.__format = struct.unpack("256I", self.raw[0:256*4])
         else:
-            self.__format = numpy.fromstring(self.raw[0:256*4], numpy.uint32)
+            self.__format = numpy.array(numpy.frombuffer(self.raw[0:256*4], numpy.uint32))
 
     def __unpack_gonio(self):
         idx= 640
diff --git a/PyMca5/PyMcaIO/PilatusCBF.py b/PyMca5/PyMcaIO/PilatusCBF.py
index 5c5ebba..9c6f260 100644
--- a/PyMca5/PyMcaIO/PilatusCBF.py
+++ b/PyMca5/PyMcaIO/PilatusCBF.py
@@ -173,24 +173,27 @@ class PilatusCBF(object):
 #                lns = len(stream)
                 idx = stream.find(key16)
                 if idx == -1:
-                    listnpa.append(np.fromstring(stream, dtype="int8"))
+                    listnpa.append(np.array(np.frombuffer(stream, dtype="int8")))
                     break
-                listnpa.append(np.fromstring(stream[:idx], dtype="int8"))
+                listnpa.append(np.array(np.frombuffer(stream[:idx], dtype="int8")))
 #                position += listnpa[-1].size
 
                 if stream[idx + 1:idx + 3] == key32:
                     if stream[idx + 3:idx + 7] == key64:
-                        listnpa.append(np.fromstring(stream[idx + 7:idx + 15], dtype="int64"))
+                        listnpa.append(np.array(np.frombuffer(stream[idx + 7:idx + 15],
+                                                              dtype="int64")))
 #                        position += 1
 #                        print "loop64 x=%4i y=%4i in idx %4i lns %4i value=%s" % ((position % 2463), (position // 2463), idx, lns, listnpa[-1])
                         shift = 15
                     else: #32 bit int
-                        listnpa.append(np.fromstring(stream[idx + 3:idx + 7], dtype="int32"))
+                        listnpa.append(np.array(np.frombuffer(stream[idx + 3:idx + 7],
+                                                              dtype="int32")))
 #                        position += 1
 #                        print "loop32 x=%4i y=%4i in idx %4i lns %4i value=%s" % ((position % 2463), (position // 2463), idx, lns, listnpa[-1])
                         shift = 7
                 else: #int16
-                    listnpa.append(np.fromstring(stream[idx + 1:idx + 3], dtype="int16"))
+                    listnpa.append(np.array(np.frombuffer(stream[idx + 1:idx + 3],
+                                                          dtype="int16")))
 #                    position += 1
 #                    print "loop16 x=%4i y=%4i in idx %4i lns %4i value=%s" % ((position % 2463), (position // 2463), idx, lns, listnpa[-1])
                     shift = 3
diff --git a/PyMca5/PyMcaIO/SpecFileStack.py b/PyMca5/PyMcaIO/SpecFileStack.py
index 01e86bc..1b51b11 100644
--- a/PyMca5/PyMcaIO/SpecFileStack.py
+++ b/PyMca5/PyMcaIO/SpecFileStack.py
@@ -2,7 +2,7 @@
 #
 # The PyMca X-Ray Fluorescence Toolkit
 #
-# Copyright (c) 2004-2017 European Synchrotron Radiation Facility
+# 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.
@@ -110,10 +110,19 @@ class SpecFileStack(DataObject.DataObject):
             iterlist = [1]
         if SLOW_METHOD and shape is None:
             self.data = numpy.zeros((self.nbFiles,
-                                     nmca / numberofdetectors,
+                                     nmca // numberofdetectors,
                                      arrRet.shape[0]),
                                      arrRet.dtype.char)
             filecounter = 0
+            if "McaLiveTime" in info:
+                nTimes = self.nbFiles * (nmca // numberofdetectors)
+                self.info["McaLiveTime"] = numpy.zeros((nTimes,),
+                                                        numpy.float32)
+            if "McaElapsedTime" in info:
+                nTimes = self.nbFiles * (nmca // numberofdetectors)
+                self.info["McaElapsedTime"] = numpy.zeros((nTimes,),
+                                                        numpy.float32)
+            nTimes = -1
             for tempFileName in filelist:
                 tempInstance = SpecFileDataSource.SpecFileDataSource(tempFileName)
                 mca_number = -1
@@ -122,16 +131,22 @@ class SpecFileStack(DataObject.DataObject):
                     numberofmca = info['NbMca']
                     if numberofmca <= 0:
                         continue
+                    # only the last mca is read
                     key = "%s.1.%s" % (keyindex, numberofmca)
                     dataObject = tempInstance._getMcaData(key)
                     arrRet = dataObject.data
                     mca_number += 1
+                    nTimes += 1
                     for i in iterlist:
                         # mcadata = scan_obj.mca(i)
                         self.data[filecounter,
                                   mca_number,
                                   :] = arrRet[:]
                         self.incrProgressBar += 1
+                        for timeKey in ["McaElapsedTime", "McaLiveTime"]:
+                            if timeKey in dataObject.info:
+                                self.info[timeKey][nTimes] = \
+                                    dataObject.info[timeKey] 
                         self.onProgress(self.incrProgressBar)
                 filecounter += 1
         elif shape is None and (self.nbFiles == 1) and (iterlist == [1]):
@@ -142,6 +157,9 @@ class SpecFileStack(DataObject.DataObject):
                                      numberofmca,
                                      arrRet.shape[0]),
                                      arrRet.dtype.char)
+            # when reading fast we do not read the time information
+            # therefore we have to remove it from the info
+            self._cleanupTimeInfo()
             for tempFileName in filelist:
                 tempInstance = specfile.Specfile(tempFileName)
                 # it can only be here if there is one scan per file
@@ -159,9 +177,12 @@ class SpecFileStack(DataObject.DataObject):
                 filecounter = 1
         elif shape is None:
             # it can only be here if there is one scan per file
+            # when reading fast we do not read the time information
+            # therefore we have to remove it from the info
+            self._cleanupTimeInfo()
             try:
                 self.data = numpy.zeros((self.nbFiles,
-                                         numberofmca / numberofdetectors,
+                                         numberofmca // numberofdetectors,
                                          arrRet.shape[0]),
                                          arrRet.dtype.char)
                 filecounter = 0
@@ -254,6 +275,8 @@ class SpecFileStack(DataObject.DataObject):
                 else:
                     raise
         else:
+            # time information not read
+            self._cleanupTimeInfo()
             sampling_order = 1
             s0 = shape[0]
             s1 = shape[1]
@@ -381,6 +404,11 @@ class SpecFileStack(DataObject.DataObject):
         self.info["NumberOfFiles"] = self.__nFiles * 1
         self.info["FileIndex"] = fileindex
 
+    def _cleanupTimeInfo(self):
+        for timeKey in ["McaElapsedTime", "McaLiveTime"]:
+            if timeKey in self.info:
+                del self.info[timeKey]
+
     def onBegin(self, n):
         pass
 
diff --git a/PyMca5/PyMcaIO/TiffIO.py b/PyMca5/PyMcaIO/TiffIO.py
index 0abf418..c564135 100644
--- a/PyMca5/PyMcaIO/TiffIO.py
+++ b/PyMca5/PyMcaIO/TiffIO.py
@@ -30,6 +30,7 @@ __author__ = "V.A. Sole - ESRF Data Analysis"
 __contact__ = "sole@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+__date__ = "25/06/2018"
 
 import sys
 import os
@@ -45,6 +46,7 @@ TAG_ID  = { 256:"NumberOfColumns",           # S or L ImageWidth
             259:"Compression",               # SHORT (1 - NoCompression, ...
             262:"PhotometricInterpretation", # SHORT (0 - WhiteIsZero, 1 -BlackIsZero, 2 - RGB, 3 - Palette color
             270:"ImageDescription",          # ASCII
+            272:"Model",                     # 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
@@ -62,6 +64,7 @@ TAG_BITS_PER_SAMPLE    = 258
 TAG_PHOTOMETRIC_INTERPRETATION = 262
 TAG_COMPRESSION        = 259
 TAG_IMAGE_DESCRIPTION  = 270
+TAG_MODEL              = 272
 TAG_STRIP_OFFSETS      = 273
 TAG_SAMPLES_PER_PIXEL  = 277
 TAG_ROWS_PER_STRIP     = 278
@@ -151,7 +154,7 @@ class TiffIO(object):
             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]
+            fortyTwo = struct.unpack(self._structChar + "H", a)[0]
             if fortyTwo != 42:
                 raise IOError("Invalid TIFF version %d" % fortyTwo)
             else:
@@ -184,7 +187,7 @@ class TiffIO(object):
         if self._access is None:
             # we do not own the file
             # open in read mode
-            newFile = open(fileName,'rb')
+            newFile = open(fileName, 'rb')
         else:
             newFile = open(fileName, self._access)
         self.fd = newFile
@@ -272,7 +275,13 @@ class TiffIO(object):
                 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]
+                    data = valueOffset[0: struct.calcsize(vfmt)]
+                    if struct.calcsize(vfmt) > len(data):
+                        # I do not see how I can enter here
+                        # Add a 0 padding to have the expected size
+                        print("WARNING: Data at tag id '%s' is smaller than expected", tagID)
+                        data = data + b"\x00" * (struct.calcsize(vfmt) - len(data))
+                    actualValue = struct.unpack(vfmt, data)[0]
                     valueOffsetList.append(actualValue)
                 else:
                     valueOffsetList.append(valueOffset)
@@ -294,8 +303,6 @@ class TiffIO(object):
                 #    print("valueOffset =  %s" % valueOffset)
         return tagIDList, fieldTypeList, nValuesList, valueOffsetList
 
-
-
     def _readIFDEntry(self, tag, tagIDList, fieldTypeList, nValuesList, valueOffsetList):
         fd = self.fd
         st = self._structChar
@@ -374,13 +381,15 @@ class TiffIO(object):
         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)
+                                       tagIDList, fieldTypeList, nValuesList,
+                                       valueOffsetList)
 
 
         if TAG_COLORMAP in tagIDList:
             idx = tagIDList.index(TAG_COLORMAP)
             tmpColormap = self._readIFDEntry(TAG_COLORMAP,
-                                          tagIDList, fieldTypeList, nValuesList, valueOffsetList)
+                                             tagIDList, fieldTypeList, nValuesList,
+                                             valueOffsetList)
             if max(tmpColormap) > 255:
                 tmpColormap = numpy.array(tmpColormap, dtype=numpy.uint16)
                 tmpColormap = (tmpColormap / 256.).astype(numpy.uint8)
@@ -423,9 +432,15 @@ class TiffIO(object):
             imageDescription = self._readIFDEntry(TAG_IMAGE_DESCRIPTION,
                     tagIDList, fieldTypeList, nValuesList, valueOffsetList)
             if type(imageDescription) in [type([1]), type((1,))]:
-                imageDescription =helpString.join(imageDescription)
+                imageDescription = helpString.join(imageDescription)
         else:
-            imageDescription = "%d/%d" % (nImage+1, len(self._IFD))
+            imageDescription = "%d/%d" % (nImage + 1, len(self._IFD))
+
+        if TAG_MODEL in tagIDList:
+            model = self._readIFDEntry(TAG_MODEL,
+                                       tagIDList, fieldTypeList, nValuesList, valueOffsetList)
+        else:
+            model = None
 
         defaultSoftware = "Unknown Software"
 
@@ -454,12 +469,15 @@ class TiffIO(object):
             date = self._readIFDEntry(TAG_DATE,
                     tagIDList, fieldTypeList, nValuesList, valueOffsetList)
             if type(date) in [type([1]), type((1,))]:
-                date =helpString.join(date)
+                date = helpString.join(date)
         else:
             date = "Unknown Date"
 
         stripOffsets = self._readIFDEntry(TAG_STRIP_OFFSETS,
-                        tagIDList, fieldTypeList, nValuesList, valueOffsetList)
+                                          tagIDList,
+                                          fieldTypeList,
+                                          nValuesList,
+                                          valueOffsetList)
         if TAG_ROWS_PER_STRIP in tagIDList:
             rowsPerStrip = self._readIFDEntry(TAG_ROWS_PER_STRIP,
                         tagIDList, fieldTypeList, nValuesList, valueOffsetList)[0]
@@ -511,6 +529,8 @@ class TiffIO(object):
         info["colormap"] = colormap
         info["sampleFormat"] = sampleFormat
         info["photometricInterpretation"] = interpretation
+        if model is not None:
+            info["model"] = model
         infoDict = {}
         testString = 'PyMca'
 
@@ -663,22 +683,24 @@ class TiffIO(object):
 
         rowStart = 0
         if len(stripOffsets) == 1:
-            bytesPerRow = int(stripByteCounts[0]/rowsPerStrip)
+            bytesPerRow = int(stripByteCounts[0] / rowsPerStrip)
+            nBytes = stripByteCounts[0]
             if nRows == rowsPerStrip:
-                actualBytesPerRow = int(image.nbytes/nRows)
+                actualBytesPerRow = int(image.nbytes / nRows)
                 if actualBytesPerRow != bytesPerRow:
                     print("Warning: Bogus StripByteCounts information")
                     bytesPerRow = actualBytesPerRow 
+                    nBytes = (rowMax-rowMin+1) * bytesPerRow
             fd.seek(stripOffsets[0] + rowMin * bytesPerRow)
-            nBytes = (rowMax-rowMin+1) * bytesPerRow
             if self._swap:
-                readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap()
+                readout = numpy.array(numpy.frombuffer(fd.read(nBytes), dtype)).byteswap()
             else:
-                readout = numpy.fromstring(fd.read(nBytes), dtype)
+                readout = numpy.array(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]
+                readout.shape = -1, nColumns, 3
             else:
                 readout.shape = -1, nColumns
             image[rowMin:rowMax+1, :] = readout
@@ -686,7 +708,7 @@ class TiffIO(object):
             for i in range(len(stripOffsets)):
                 # the amount of rows
                 nRowsToRead = rowsPerStrip
-                rowEnd = int(min(rowStart+nRowsToRead, nRows))
+                rowEnd = int(min(rowStart + nRowsToRead, nRows))
                 if rowEnd < rowMin:
                     rowStart += nRowsToRead
                     continue
@@ -707,25 +729,27 @@ class TiffIO(object):
                     # intermediate buffer
                     tmpBuffer = fd.read(nBytes)
                     while readBytes < nBytes:
-                        n = struct.unpack('b', tmpBuffer[readBytes:(readBytes+1)])[0]
+                        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)
+                                                      readBytes + (n + 1)]
+                            readBytes += (n + 1)
                         elif n > -128:
-                            bufferBytes += (-n+1) * tmpBuffer[readBytes:(readBytes+1)]
+                            bufferBytes += (-n + 1) * \
+                                           tmpBuffer[readBytes:(readBytes + 1)]
                             readBytes += 1
                         else:
                             # if read -128 ignore the byte
                             continue
                     if self._swap:
-                        readout = numpy.fromstring(bufferBytes, dtype).byteswap()
+                        readout = numpy.array(numpy.frombuffer(bufferBytes, dtype)).byteswap()
                     else:
-                        readout = numpy.fromstring(bufferBytes, dtype)
+                        readout = numpy.array(numpy.frombuffer(bufferBytes, dtype))
                     if hasattr(nBits, 'index'):
                         readout.shape = -1, nColumns, len(nBits)
                     elif info['colormap'] is not None:
@@ -738,9 +762,9 @@ class TiffIO(object):
                     if 1:
                         # use numpy
                         if self._swap:
-                            readout = numpy.fromstring(fd.read(nBytes), dtype).byteswap()
+                            readout = numpy.array(numpy.frombuffer(fd.read(nBytes), dtype)).byteswap()
                         else:
-                            readout = numpy.fromstring(fd.read(nBytes), dtype)
+                            readout = numpy.array(numpy.frombuffer(fd.read(nBytes), dtype))
                         if hasattr(nBits, 'index'):
                             readout.shape = -1, nColumns, len(nBits)
                         elif colormap is not None:
@@ -773,8 +797,8 @@ class TiffIO(object):
                          image[:, :, 1] * 0.587 + \
                          image[:, :, 2] * 0.299).astype(numpy.float32)
 
-        if (rowMin == 0) and (rowMax == (nRows-1)):
-            self._imageDataCacheIndex.insert(0,nImage)
+        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]
@@ -1034,7 +1058,7 @@ class TiffIO(object):
                               bitsPerSample * nChannels / 8)
 
         if descriptionLength > 4:
-            stripOffsets0 = endOfFile + dateLength + descriptionLength +\
+            stripOffsets0 = endOfFile + dateLength + descriptionLength + \
                         2 + 12 * nDirectoryEntries + 4
         else:
             stripOffsets0 = endOfFile + dateLength + \
@@ -1063,7 +1087,7 @@ class TiffIO(object):
                 value = stripOffsets0 + i * stripByteCounts
                 stripOffsets.append(value)
                 if i == 0:
-                    stripOffsetsString  = struct.pack(fmt, value)
+                    stripOffsetsString = struct.pack(fmt, value)
                     stripByteCountsString = struct.pack(fmt, stripByteCounts)
                 else:
                     stripOffsetsString += struct.pack(fmt, value)
@@ -1269,7 +1293,7 @@ if __name__ == "__main__":
         tif = None
         if os.path.exists(filename):
             print("Testing image appending")
-            tif = TiffIO(filename, mode = 'rb+')
+            tif = TiffIO(filename, mode='rb+')
             tif.writeImage((data * 2).astype(dtype), info={'Title': '2nd'})
             tif = None
     tif = TiffIO(filename)