new scripts

imagej_tiffwriter.py

+#!/usr/bin/env python3
+
+'''
+/**
+ * @file imagej_tiff_saver.py
+ * @brief save tiffs for imagej (1.52d+) - with stacks and hyperstacks
+ * @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, TiffImagePlugin
+import numpy as np
+import math
+
+def __get_IJ_IFD(t,z,c):
+
+  ifd = TiffImagePlugin.ImageFileDirectory_v2()
+  #is_hyperstack = 'true' if len(shape)>1 else 'false'
+  #if (len(shape)>0):
+  return ifd
+
+
+def save(path,images,force_stack=False,force_hyperstack=False):
+
+  # Got images, analyze shape:
+  #   - possible formats (c == depth):
+  #     -- (t,z,h,w,c)
+  #     -- (t,h,w,c), t or z does not matter
+  #     -- (h,w,c)
+  #     -- (h,w)
+
+  # save single layer image
+  if   len(images.shape)==2:
+    # (h,w) -> (h,w,c=1)
+    images = images[:,:,np.newaxis]
+  elif len(images.shape)>2:
+    # do nothing
+    pass
+  else:
+    # (w,) -> (h=1,w,c=1)
+    images = images[np.newaxis,:,np.newaxis]
+
+  #imlist = np.ravel(Image.fromarray(images))
+  t,z,h,w,c  = images.shape
+  c_axis = len(images.shape)-1
+  channels = np.squeeze(np.split(images,c,axis=c_axis))
+
+  split_channels = np.concatenate(channels,axis=-3)
+  images_flat = np.reshape(split_channels,(-1,h,w))
+
+  imlist = []
+  for i in range(images_flat.shape[0]):
+    imlist.append(Image.fromarray(images_flat[i]))
+
+  imlist[0].save(path,save_all=True,append_images=imlist[1:],tiffinfo=__get_IJ_IFD(t,z,c))
+
+# Testing
+if __name__ == "__main__":
+
+
+  def hamming_window(x,N):
+    y = 0.54 - 0.46*math.cos(2*math.pi*x/(N-1))
+    return y
+
+  hw = hamming_window
+
+  NT = 5
+  NC = 2
+  NZ = 3
+  NX = 512
+  NY = 512
+
+  images = np.empty((NT,NZ,NY,NX,NC))
+
+  import time
+  print(str(time.time())+": Generating test images")
+  for t in range(NT):
+    for z in range(NZ):
+      for c in range(NC):
+        images[t,z,:,:,c] = np.array([[(255-t*25)*hw(i,512)*hw(j,512) for i in range(NX)] for j in range(NY)],np.float32)
+  print(str(time.time())+": Test images generated")
+  print("Images shape: "+str(images.shape))
+
+  v = save("result_2.tiff",images)

test_nn_infer.py

+#!/usr/bin/env python3
+
+__copyright__ = "Copyright 2018, Elphel, Inc."
+__license__   = "GPL-3.0+"
+__email__     = "oleg@elphel.com"
+
+'''
+Open all tiffs in a folder, combine a single tiff from randomly selected
+tiles from originals
+'''
+
+from PIL import Image
+
+import os
+import sys
+import glob
+
+import imagej_tiff as ijt
+import pack_tile as pile
+
+import numpy as np
+import itertools
+
+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'
+
+
+def print_time():
+  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)
+
+# USAGE: python3 test_3.py some-path
+
+VALUES_LAYER_NAME = 'other'
+LAYERS_OF_INTEREST = ['diagm-pair', 'diago-pair', 'hor-pairs', 'vert-pairs']
+RADIUS = 1
+
+try:
+  src = sys.argv[1]
+except IndexError:
+  src = "."
+
+print("Importing TensorCrawl")
+print_time()
+
+import tensorflow as tf
+import tensorflow.contrib.slim as slim
+
+print("TensorCrawl imported")
+print_time()
+
+result_dir = './result/'
+checkpoint_dir = './result/'
+save_freq = 500
+
+def lrelu(x):
+    return tf.maximum(x*0.2,x)
+
+def network(input):
+
+  fc1 = slim.fully_connected(input,101,activation_fn=lrelu,scope='g_fc1')
+  fc2 = slim.fully_connected(fc1,  101,activation_fn=lrelu,scope='g_fc2')
+  fc3 = slim.fully_connected(fc2,  101,activation_fn=lrelu,scope='g_fc3')
+  fc4 = slim.fully_connected(fc3,  101,activation_fn=lrelu,scope='g_fc4')
+  fc5 = slim.fully_connected(fc4,    2,activation_fn=lrelu,scope='g_fc5')
+
+  return fc5
+
+
+sess = tf.Session()
+
+in_tile = tf.placeholder(tf.float32,[None,101])
+gt      = tf.placeholder(tf.float32,[None,2])
+out = network(in_tile)
+
+#G_loss = tf.reduce_mean(tf.abs(out[:,0]-gt[:,0]))
+#t_vars=tf.trainable_variables()
+#lr=tf.placeholder(tf.float32)
+#G_opt=tf.train.AdamOptimizer(learning_rate=lr).minimize(G_loss,var_list=[var for var in t_vars if #var.name.startswith('g_')])
+
+saver=tf.train.Saver()
+sess.run(tf.global_variables_initializer())
+ckpt=tf.train.get_checkpoint_state(checkpoint_dir)
+if ckpt:
+  print('loaded '+ckpt.model_checkpoint_path)
+  saver.restore(sess,ckpt.model_checkpoint_path)
+
+# do not need output for now
+#if not os.path.isdir(result_dir + 'final/'):
+#    os.makedirs(result_dir + 'final/')
+
+tlist = glob.glob(src+"/*.tiff")
+
+print("\n".join(tlist))
+print("Found "+str(len(tlist))+" preprocessed tiff files:")
+print_time()
+''' WARNING, assuming:
+      - timestamps and part of names match
+      - layer order and names are identical
+'''
+
+# Now PROCESS
+for item in tlist:
+  print(bcolors.OKGREEN+"Processing "+item+bcolors.ENDC)
+  # open the first one to get dimensions and other info
+  tiff = ijt.imagej_tiff(item)
+
+  # shape as tiles? make a copy or make writeable
+  # (242, 324, 9, 9, 5)
+
+  # get labels
+  labels = tiff.labels.copy()
+  labels.remove(VALUES_LAYER_NAME)
+
+  print("Image data layers:  "+str(labels))
+  print("Layers of interest: "+str(LAYERS_OF_INTEREST))
+  print("Values layer: "+str([VALUES_LAYER_NAME]))
+
+  # create copies
+  tiles  = np.copy(tiff.getstack(labels,shape_as_tiles=True))
+  # need values? Well, just to compare
+  values = np.copy(tiff.getvalues(label=VALUES_LAYER_NAME))
+  #gt = values[:,:,1:3]
+
+  print("Mixed tiled input data shape: "+str(tiles.shape))
+  #print_time()
+
+  # now pack from 9x9 to 1x25
+  # tiles and values
+
+  # Parse packing table
+  # packing table name
+  ptab_name = "tile_packing_table.xml"
+  ptab = pile.PackingTable(ptab_name,LAYERS_OF_INTEREST).lut
+
+  # might not need it because going to loop through anyway
+  packed_tiles = np.array([[pile.pack_tile(tiles[i,j],ptab) for j in range(tiles.shape[1])] for i in range(tiles.shape[0])])
+  packed_tiles = np.dstack((packed_tiles,values[:,:,0]))
+
+  # flatten
+  packed_tiles_flat = packed_tiles.reshape(-1, packed_tiles.shape[-1])
+  values_flat       = values.reshape(-1, values.shape[-1])
+
+  print("Packed (81x4 -> 1x(25*4+1)) tiled input shape: "+str(packed_tiles_flat.shape))
+  print("Values shape "+str(values_flat.shape))
+  print_time()
+
+  # now run prediction
+  output = sess.run(out,feed_dict={in_tile:packed_tiles_flat})
+
+  print("Output shape: "+str(output.shape))
+
+  # so, let's print
+  for i in range(output.shape[0]):
+    p  = output[i,0]
+    pc = output[i,1]
+    fv = values_flat[i,0]
+    gt = values_flat[i,1]
+    cf = values_flat[i,2]
+
+    vstring = "["+"{0:.2f}".format(fv)+", "+"{0:.2f}".format(gt)+", "+"{0:.2f}".format(cf)+"]"
+    pstring = "["+"{0:.2f}".format(p)+", "+"{0:.2f}".format(pc)+"]"
+
+    if not np.isnan(p):
+      outstring = "i: "+str(i)+"    Values:  "+vstring+"    Prediction:  "+pstring
+      if cf<0.5:
+        print(outstring)
+      else:
+        print(bcolors.WARNING+outstring+bcolors.ENDC)
+
+    #else:
+    #  print("i: "+str(i)+" NaNs")
+
+# check histogram:
+
+
+#import matplotlib.pyplot as plt
+
+#x = np.histogram(values_flat[:,2])
+#plt.hist(x, bins=100)
+#plt.ylabel('Confidence')
+
+print_time()
+print(bcolors.OKGREEN+"time: "+str(time.time())+bcolors.ENDC)
+
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test_plot_disp_and_confidence.py

+#!/usr/bin/env python3
+
+__copyright__ = "Copyright 2018, Elphel, Inc."
+__license__   = "GPL-3.0+"
+__email__     = "oleg@elphel.com"
+
+'''
+Open all tiffs in a folder, combine a single tiff from randomly selected
+tiles from originals
+'''
+
+from PIL import Image
+
+import os
+import sys
+import glob
+
+import imagej_tiff as ijt
+import pack_tile as pile
+
+import numpy as np
+import itertools
+
+import time
+
+import matplotlib.pyplot as plt
+
+#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'
+
+
+def print_time():
+  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)
+
+# USAGE: python3 test_3.py some-path
+
+VALUES_LAYER_NAME = 'other'
+LAYERS_OF_INTEREST = ['diagm-pair', 'diago-pair', 'hor-pairs', 'vert-pairs']
+RADIUS = 1
+
+try:
+  src = sys.argv[1]
+except IndexError:
+  src = "."
+
+
+tlist = glob.glob(src+"/*.tiff")
+
+print("\n".join(tlist))
+print("Found "+str(len(tlist))+" preprocessed tiff files:")
+print_time()
+''' WARNING, assuming:
+      - timestamps and part of names match
+      - layer order and names are identical
+'''
+
+# Now PROCESS
+for item in tlist:
+  print(bcolors.OKGREEN+"Processing "+item+bcolors.ENDC)
+  # open the first one to get dimensions and other info
+  tiff = ijt.imagej_tiff(item)
+
+  # shape as tiles? make a copy or make writeable
+  # (242, 324, 9, 9, 5)
+
+  # get labels
+  labels = tiff.labels.copy()
+  labels.remove(VALUES_LAYER_NAME)
+
+  print("Image data layers:  "+str(labels))
+  print("Layers of interest: "+str(LAYERS_OF_INTEREST))
+  print("Values layer: "+str([VALUES_LAYER_NAME]))
+
+  # create copies
+  #tiles  = np.copy(tiff.getstack(labels,shape_as_tiles=True))
+  # need values? Well, just to compare
+  values = np.copy(tiff.getvalues(label=VALUES_LAYER_NAME))
+  #gt = values[:,:,1:3]
+
+  print("Mixed tiled input data shape: "+str(values.shape))
+
+  # plot ground truth
+  values[values==-256] = np.nan
+
+  t = values[:,:,1]
+  mytitle = "Ground truth"
+  fig = plt.figure()
+  fig.canvas.set_window_title(mytitle)
+  fig.suptitle(mytitle)
+  plt.imshow(t)
+  plt.colorbar()
+  #plt.show()
+
+  t = values[:,:,2]
+  mytitle = "Confidence"
+  fig = plt.figure()
+  fig.canvas.set_window_title(mytitle)
+  fig.suptitle(mytitle)
+  plt.imshow(t)
+  plt.colorbar()
+  #plt.show()
+
+  mytitle = "Confidence histogram"
+  fig = plt.figure()
+  fig.canvas.set_window_title(mytitle)
+  fig.suptitle(mytitle)
+
+  values_flat = np.ravel(values[:,:,2])
+  #values_flat[values_flat==0] = np.nan
+
+  # flat and filtered
+  values_ff = values_flat[values_flat!=0]
+  values_ff = np.round(values_ff,3)
+
+  plt.hist(values_ff,bins=1000)
+  plt.ylabel('N')
+
+  plt.show()
+
+
+print_time()
+print(bcolors.OKGREEN+"time: "+str(time.time())+bcolors.ENDC)
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test_tf_ops.py

+#!/usr/bin/env python3
+
+import time
+import numpy as np
+
+#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'
+
+
+def print_time():
+  print(bcolors.BOLDWHITE+"time: "+str(time.time())+bcolors.ENDC)
+
+
+# MAIN
+print("Importing TensorCrawl")
+print_time()
+
+import tensorflow as tf
+import tensorflow.contrib.slim as slim
+
+print("TensorCrawl imported")
+print_time()
+
+sess = tf.Session()
+
+# (10,)
+a_in = [0,1,2,3,4,5,6,7,8,9]
+# (1,)
+b_in = [1.5]
+# (3,2)
+c_in = [
+  [0.1,0.2],
+  [0.3,0.4],
+  [0.5,0.6]
+]
+
+#print(np.array(a_in).shape)
+
+a = tf.placeholder(tf.float32,[None,10])
+b = tf.placeholder(tf.float32,[None,1])
+
+c = tf.concat([a,b],axis=1)
+
+#d = tf.constant(-1.0)
+e = tf.maximum(a-1.0,0.0)
+
+f = tf.placeholder(tf.float32,[None,3,2])
+
+g = tf.maximum(f[:,:,1]+0.01,0)
+
+res = sess.run(g,feed_dict={a:[a_in],b:[b_in],f:[c_in]})
+#res = sess.run(a,feed_dict={a:a_in})
+
+print(res.shape)
+print(res)
+
+print_time()
+print(bcolors.OKGREEN+"time: "+str(time.time())+bcolors.ENDC)
\ No newline at end of file