Commit 843fef56 authored by Oleg Dzhimiev's avatar Oleg Dzhimiev
Browse files

1. parse xml data 

2. stack tiles
3. 8bpp and 32bpp
4. extract values from specific layer named 'other'
5. test 8bpp against corresponding 32bpp
parent 10df8116

imagej_tiff.py

+181 −32
Original line number Original line Diff line number Diff line 
#!/usr/bin/env python3

#!/usr/bin/env python3





'''

/**

 * @file imagej_tiff.py

 * @brief open multi layer tiff files, display layers and parse meta data

 * @par <b>License</b>:

 *  This program is free software: you can redistribute it and/or modify

 *  it under the terms of the GNU General Public License as published by

 *  the Free Software Foundation, either version 3 of the License, or

 *  (at your option) any later version.

 *

 *  This program is distributed in the hope that it will be useful,

 *  but WITHOUT ANY WARRANTY; without even the implied warranty of

 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *  GNU General Public License for more details.

 *

 *  You should have received a copy of the GNU General Public License

 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.

*/

'''



__copyright__ = "Copyright 2018, Elphel, Inc."

__license__   = "GPL-3.0+"

__email__     = "oleg@elphel.com"



from PIL import Image

from PIL import Image

import xml.etree.ElementTree as ET

import xml.etree.ElementTree as ET

import numpy as np

import numpy as np

import matplotlib.pyplot as plt

import matplotlib.pyplot as plt





import sys

import xml.dom.minidom as minidom



import time



#http://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-python

class bcolors:

    HEADER = '\033[95m'

    OKBLUE = '\033[94m'

    OKGREEN = '\033[92m'

    WARNING = '\033[38;5;214m'

    FAIL = '\033[91m'

    ENDC = '\033[0m'

    BOLD = '\033[1m'

    BOLDWHITE = '\033[1;37m'

    UNDERLINE = '\033[4m'



# reshape to tiles

def get_tile_images(image, width=8, height=8):

  _nrows, _ncols, depth = image.shape

  _size = image.size

  _strides = image.strides



  nrows, _m = divmod(_nrows, height)

  ncols, _n = divmod(_ncols, width)

  if _m != 0 or _n != 0:

    return None



  return np.lib.stride_tricks.as_strided(

    np.ravel(image),

    shape=(nrows, ncols, height, width, depth),

    strides=(height * _strides[0], width * _strides[1], *_strides),

    writeable=False

  )



# TiffFile has no len exception

# TiffFile has no len exception

#import imageio

#import imageio
@@ -67,6 +78,12 @@ class imagej_tiff: 
    self.labels = []

    self.labels = []

    # infos will contain xml data Elphel stores in some of tiff files

    # infos will contain xml data Elphel stores in some of tiff files

    self.infos = []

    self.infos = []

    # dictionary from decoded infos[0] xml data

    self.props = {}



    # bits per sample, type int

    self.bpp = tif.tag[258][0]



    self.__split_labels(tif.n_frames,tif.tag)

    self.__split_labels(tif.n_frames,tif.tag)

    self.__parse_info()

    self.__parse_info()

    # image layers stacked along depth - (think RGB)

    # image layers stacked along depth - (think RGB)
@@ -77,7 +94,21 @@ class imagej_tiff: 
      tif.seek(i)

      tif.seek(i)

      a = np.array(tif)

      a = np.array(tif)

      a = np.reshape(a,(a.shape[0],a.shape[1],1))

      a = np.reshape(a,(a.shape[0],a.shape[1],1))



      #a = a[:,:,np.newaxis]

      #a = a[:,:,np.newaxis]



      # scale for 8-bits

      # exclude layer named 'other'

      if self.bpp==8:

        _min = self.data_min

        _max = self.data_max

        _MIN = 1

        _MAX = 255

        a = a.astype(float)

        if self.labels[i]!='other':

          a[a==0]=np.nan

          a = (_max-_min)*(a-_MIN)/(_MAX-_MIN)+_min



      # init

      # init

      if i==0:

      if i==0:

        self.image = a

        self.image = a
@@ -88,12 +119,37 @@ class imagej_tiff: 
    # init done, close the image

    # init done, close the image

    tif.close()

    tif.close()





  # label == tiff layer name

  def getvalues(self,label=""):

    l = self.getstack([label],shape_as_tiles=True)

    res = np.empty((l.shape[0],l.shape[1],3))



    for i in range(res.shape[0]):

      for j in range(res.shape[1]):

        # 9x9 -> 81x1

        m = np.ravel(l[i,j])

        if self.bpp==32:

          res[i,j,0] = m[0]

          res[i,j,1] = m[2]

          res[i,j,2] = m[4]

        elif self.bpp==8:

          res[i,j,0] = ((m[0]-128)*256+m[1])/128

          res[i,j,1] = ((m[2]-128)*256+m[3])/128

          res[i,j,2] = (m[4]*256+m[5])/65536.0

        else:

          res[i,j,0] = np.nan

          res[i,j,1] = np.nan

          res[i,j,2] = np.nan



    return res





  # get ordered stack of images by provided items

  # get ordered stack of images by provided items

  # by index or label name

  # by index or label name

  def getstack(self,items=[]):

  def getstack(self,items=[],shape_as_tiles=False):

    a = ()

    a = ()

    if len(items)==0:

    if len(items)==0:

      return self.image

      b = self.image

    else:

    else:

      for i in items:

      for i in items:

        if type(i)==int:

        if type(i)==int:
@@ -102,8 +158,12 @@ class imagej_tiff: 
          j = self.labels.index(i)

          j = self.labels.index(i)

          a += (self.image[:,:,j],)

          a += (self.image[:,:,j],)

      # stack along depth

      # stack along depth

      return np.stack(a,axis=2)

      b = np.stack(a,axis=2)





    if shape_as_tiles:

      b = get_tile_images(b,self.tileW,self.tileH)



    return b





  # get np.array of a channel

  # get np.array of a channel

  # * do not handle out of bounds

  # * do not handle out of bounds
@@ -152,7 +212,7 @@ class imagej_tiff: 
    #tmp_im.show()

    #tmp_im.show()









  # puts etrees in infos

  # puts etrees in infoss

  def __parse_info(self):

  def __parse_info(self):





    infos = []

    infos = []
@@ -161,6 +221,21 @@ class imagej_tiff: 




    self.infos = infos

    self.infos = infos





    # specifics

    # properties dictionary

    pd = {}



    for child in infos[0]:

      #print(child.tag+"::::::"+child.text)

      pd[child.tag] = child.text



    self.props = pd



    # tiles are squares

    self.tileW = int(self.props['tileWidth'])

    self.tileH = int(self.props['tileWidth'])

    self.data_min = float(self.props['data_min'])

    self.data_max = float(self.props['data_max'])





  # makes arrays of labels (strings) and unparsed xml infos

  # makes arrays of labels (strings) and unparsed xml infos

  def __split_labels(self,n,tag):

  def __split_labels(self,n,tag):
@@ -188,24 +263,98 @@ class imagej_tiff: 
        skip -= 1

        skip -= 1

      tag_labels = tag_labels[l:]

      tag_labels = tag_labels[l:]







#MAIN

#MAIN

if __name__ == "__main__":

if __name__ == "__main__":



  try:

    fname = sys.argv[1]

  except IndexError:

    fname = "1521849031_093189-ML_DATA-32B-O-OFFS1.0.tiff"

    fname = "1521849031_093189-ML_DATA-08B-O-OFFS1.0.tiff"



  #fname = "1521849031_093189-DISP_MAP-D0.0-46.tif"

  #fname = "1521849031_093189-DISP_MAP-D0.0-46.tif"

  fname = "test.tiff"

  #fname = "1526905735_662795-ML_DATA-08B-AIOTD-OFFS2.0.tiff"

  #fname = "test.tiff"



  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)





  ijt = imagej_tiff(fname)

  ijt = imagej_tiff(fname)





  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)



  print(ijt.labels)

  print(ijt.labels)

  print(ijt.infos)

  print(ijt.infos)



  rough_string = ET.tostring(ijt.infos[0], "utf-8")

  reparsed = minidom.parseString(rough_string)

  print(reparsed.toprettyxml(indent="\t"))



  print(ijt.props)



  # needed properties:

  print("Tiles shape: "+str(ijt.tileW)+"x"+str(ijt.tileH))

  print("Data min: "+str(ijt.data_min))

  print("Data max: "+str(ijt.data_max))



  print(ijt.image.shape)

  print(ijt.image.shape)





  #ijt.show_images()

  # layer order: ['diagm-pair', 'diago-pair', 'hor-pairs', 'vert-pairs', 'other']

  # now split this into tiles:



  #tiles = get_tile_images(ijt.image,ijt.tileW,ijt.tileH)

  #print(tiles.shape)



  tiles = ijt.getstack(['diagm-pair','diago-pair','hor-pairs','vert-pairs'],shape_as_tiles=True)

  print("Stack of images shape: "+str(tiles.shape))



  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)

  # provide layer name

  values = ijt.getvalues(label='other')

  print("Stack of values shape: "+str(values.shape))



  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)

  #print(values)



  #print(value_tiles[131,162].flatten())

  #print(np.ravel(value_tiles[131,162]))



  #values = np.empty((vt.shape[0],vt.shape[1],3))



  #for i in range(values.shape[0]):

  #  for j in range(values.shape[1]):

  #    values[i,j,0] = get_v1()





  #print(tiles[121,160,:,:,0].shape)

  #_nrows = int(ijt.image.shape[0] / ijt.tileH)

  #_ncols = int(ijt.image.shape[1] / ijt.tileW)

  #_nrows = 32

  #_ncols = 32

  #print(str(_nrows)+" "+str(_ncols))

  #fig, ax = plt.subplots(nrows=_nrows, ncols=_ncols)

  #for i in range(_nrows):

  #  for j in range(_ncols):

  #    ax[i,j].imshow(tiles[i+100,j,:,:,0])

  #    ax[i,j].set_axis_off()



  #for i in range(5):

  #  fig = plt.figure()

  #  plt.imshow(tiles[121,160,:,:,i])

  #  plt.colorbar()



  #ijt.show_images(['other'])





  #ijt.show_images([0,3])

  #ijt.show_images([0,3])

  ijt.show_images(['X-corr','Y-corr'])

  #ijt.show_images(['X-corr','Y-corr'])

  #ijt.show_images(['R-vign',3])

  #ijt.show_images(['R-vign',3])





  plt.show()

  #ijt.show_images()

  #plt.show()













  # Examples

  # Examples

test_8bpp_vs_32bpp.py

0 → 100644
+155 −0
Original line number Original line Diff line number Diff line 
#!/usr/bin/env python3



from PIL import Image

import xml.etree.ElementTree as ET

import numpy as np

import matplotlib.pyplot as plt



import sys

import xml.dom.minidom as minidom



import time



from imagej_tiff import imagej_tiff



fname08bpp = "1521849031_093189-ML_DATA-08B-O-OFFS1.0.tiff"

fname32bpp = "1521849031_093189-ML_DATA-32B-O-OFFS1.0.tiff"



im08 = imagej_tiff(fname08bpp)

im32 = imagej_tiff(fname32bpp)



print(im08.props)



THRESHOLD = 0.01

THRESHOLD2 = 0.1



values08 = im08.getvalues(label='other')

values32 = im32.getvalues(label='other')



# compare values



print("test1: Compare values layers")



values32[np.isnan(values32)] = 0

values08[np.isnan(values08)] = 0

values08[values08==-256.0] = 0



delta = abs(values32 - values08)

#print(delta)

#print(delta.shape)



error_counter = 0

for i in range(delta.shape[0]):

  for j in range(delta.shape[1]):

    for k in range(delta.shape[2]):

      if delta[i,j,k]>THRESHOLD:

        error_counter += 1

        print("Fail ("+str(error_counter)+"): "+str((i,j,k))+" "+str(delta[i,j,k]))

        print(str(values32[i,j,k])+" vs "+str(values08[i,j,k]))



if error_counter==0:

  print("Values are OK")



#v08 = im08.getstack(['other'],shape_as_tiles=True)

#v32 = im32.getstack(['other'],shape_as_tiles=True)



#print(v08.shape)



#_nrows = 1

#_ncols = 1



#fig = plt.figure()

#plt.imshow(v08[241,321,:,:,0])

#plt.colorbar()



#fig = plt.figure()

#plt.imshow(v32[241,321,:,:,0])

#plt.colorbar()



# compare layers



print("test2: Compare layers")



tiles08 = im08.getstack(['diagm-pair','diago-pair','hor-pairs','vert-pairs'],shape_as_tiles=True)

tiles32 = im32.getstack(['diagm-pair','diago-pair','hor-pairs','vert-pairs'],shape_as_tiles=True)



delta2 = abs(tiles32-tiles08)

error_counter = 0

for i in range(delta2.shape[0]):

  for j in range(delta2.shape[1]):

    for k in range(delta2.shape[2]):

      for l in range(delta2.shape[3]):

        for m in range(delta2.shape[4]):

          if delta2[i,j,k,l,m]>THRESHOLD2:

            error_counter += 1

            print("Fail ("+str(error_counter)+"): "+str((i,j,k,l,m))+" "+str(delta2[i,j,k,l,m]))

            print(str(tiles32[i,j,k,l,m])+" vs "+str(tiles08[i,j,k,l,m]))



if error_counter==0:

  print("Layers are OK")



#fig = plt.figure()

#plt.imshow(tiles08[121,187,:,:,1])

#plt.colorbar()



#fig = plt.figure()

#plt.imshow(tiles32[121,187,:,:,1])

#plt.colorbar()



plt.show()