Merge branch 'master' of git.elphel.com:Elphel/python3-imagej-tiff

nn_ds_neibs16.py

 #!/usr/bin/env python3
-from numpy import float64
-from tensorflow.contrib.losses.python.metric_learning.metric_loss_ops import npairs_loss
-from debian.deb822 import PdiffIndex
+##from numpy import float64
+##from tensorflow.contrib.losses.python.metric_learning.metric_loss_ops import npairs_loss
+##from debian.deb822 import PdiffIndex
 
 __copyright__ = "Copyright 2018, Elphel, Inc."
 __license__   = "GPL-3.0+"
 __email__     = "andrey@elphel.com"
 
 
-from PIL import Image
+##from PIL import Image
 
 import os
 import sys
-import glob
+##import glob
 
 import numpy as np
-import itertools
+##import itertools
 
 import time
 
-import matplotlib.pyplot as plt
+##import matplotlib.pyplot as plt
 
 import shutil
 from threading import Thread
@@ -49,7 +49,7 @@ except IndexError:
     root_dir =  os.path.dirname(conf_file)
     
 print ("Configuration file: " + conf_file)
-parameters, dirs, files = qsf.parseXmlConfig(conf_file, root_dir)
+parameters, dirs, files, _ = qsf.parseXmlConfig(conf_file, root_dir)
 """
 Temporarily for backward compatibility
 """
@@ -221,7 +221,7 @@ if SPREAD_CONVERGENCE:
                                             
 else:
     outs, inp_weights =  qcstereo_network.networks_siam(
-                                            input=              corr2d_Nx325,
+                                            input_tensor=       corr2d_Nx325,
                                             input_global =      None,
                                             layout1 =           NN_LAYOUT1, 
                                             layout2 =           NN_LAYOUT2,
@@ -247,7 +247,7 @@ G_losses[0], _disp_slice, _d_gt_slice, _out_diff, _out_diff2, _w_norm, _out_wdif
               absolute_disparity =     ABSOLUTE_DISPARITY,
               use_confidence =         USE_CONFIDENCE, # True, 
               lambda_conf_avg =        0.01,
-              lambda_conf_pwr =        0.1,
+##              lambda_conf_pwr =        0.1,
               conf_pwr =               2.0,
               gt_conf_offset =         0.08,
               gt_conf_pwr =            2.0,
@@ -268,7 +268,7 @@ for n in range (1,len(partials)):
               absolute_disparity =     ABSOLUTE_DISPARITY,
               use_confidence =         USE_CONFIDENCE, # True, 
               lambda_conf_avg =        0.01,
-              lambda_conf_pwr =        0.1,
+#              lambda_conf_pwr =        0.1,
               conf_pwr =               2.0,
               gt_conf_offset =         0.08,
               gt_conf_pwr =            2.0,
@@ -702,7 +702,7 @@ with tf.Session()  as sess:
                 if ntest > 0:
                     image_data[ntest] = None
      
-     # Close writers
+    # Close writers
     train_writer.close()
     test_writer.close()
     test_writer1.close()

nn_eval_01.py

+#!/usr/bin/env python3
+
+__copyright__ = "Copyright 2018, Elphel, Inc."
+__license__   = "GPL-3.0+"
+__email__     = "andrey@elphel.com"
+
+
+from PIL import Image
+
+import os
+import sys
+import glob
+
+import numpy as np
+
+import time
+
+import matplotlib.pyplot as plt
+
+import qcstereo_functions as qsf
+
+#import xml.etree.ElementTree as ET
+
+qsf.TIME_START = time.time()
+qsf.TIME_LAST  = qsf.TIME_START
+
+IMG_WIDTH =        324 # tiles per image row
+DEBUG_LEVEL= 1
+
+try:
+    conf_file =  sys.argv[1]
+except IndexError:
+    print("Configuration path is required as a first argument. Optional second argument specifies root directory for data files")
+    exit(1)
+try:
+    root_dir =  sys.argv[2]
+except IndexError:
+    root_dir =  os.path.dirname(conf_file)
+    
+print ("Configuration file: " + conf_file)
+parameters, dirs, files, dbg_parameters = qsf.parseXmlConfig(conf_file, root_dir)
+"""
+Temporarily for backward compatibility
+"""
+if not "SLOSS_CLIP" in parameters:
+    parameters['SLOSS_CLIP'] = 0.5
+    print ("Old config, setting SLOSS_CLIP=", parameters['SLOSS_CLIP'])
+    
+"""
+Defined in config file
+"""
+TILE_SIDE, TILE_LAYERS, TWO_TRAINS, NET_ARCH1, NET_ARCH2 = [None]*5
+ABSOLUTE_DISPARITY,SYM8_SUB, WLOSS_LAMBDA,  SLOSS_LAMBDA, SLOSS_CLIP  = [None]*5
+SPREAD_CONVERGENCE, INTER_CONVERGENCE, HOR_FLIP, DISP_DIFF_CAP, DISP_DIFF_SLOPE  = [None]*5
+CLUSTER_RADIUS,ABSOLUTE_DISPARITY = [None]*2
+    
+globals().update(parameters)
+
+
+#exit(0)
+
+
+TILE_SIZE =         TILE_SIDE* TILE_SIDE # == 81
+FEATURES_PER_TILE =  TILE_LAYERS * TILE_SIZE# == 324
+BATCH_SIZE =       ([1,2][TWO_TRAINS])*2*1000//25 # == 80 Each batch of tiles has balanced D/S tiles, shuffled batches but not inside batches
+
+SUFFIX=(str(NET_ARCH1)+'-'+str(NET_ARCH2)+
+       (["R","A"][ABSOLUTE_DISPARITY]) +
+       (["NS","S8"][SYM8_SUB])+
+       "WLAM"+str(WLOSS_LAMBDA)+
+       "SLAM"+str(SLOSS_LAMBDA)+
+       "SCLP"+str(SLOSS_CLIP)+
+       (['_nG','_G'][SPREAD_CONVERGENCE])+
+       (['_nI','_I'][INTER_CONVERGENCE]) +
+       (['_nHF',"_HF"][HOR_FLIP]) +
+       ('_CP'+str(DISP_DIFF_CAP)) +
+       ('_S'+str(DISP_DIFF_SLOPE))
+       )
+
+##############################################################################
+cluster_size = (2 * CLUSTER_RADIUS + 1) * (2 * CLUSTER_RADIUS + 1)
+center_tile_index = 2 * CLUSTER_RADIUS * (CLUSTER_RADIUS + 1)
+qsf.prepareFiles(dirs, files, suffix = SUFFIX)
+
+#import tensorflow.contrib.slim as slim
+NN_DISP =   0
+HEUR_DISP = 1
+GT_DISP =   2
+GT_CONF =   3
+NN_NAN =    4
+HEUR_NAN =  5
+NN_DIFF =   6
+HEUR_DIFF = 7
+CONF_MAX = 0.7
+ERR_AMPL = 0.3
+TIGHT_TOP = 0.95
+TIGHT_HPAD = 1.0
+TIGHT_WPAD = 1.0
+FIGSIZE = [8.5,11.0]
+WOI_COLOR = "red"
+
+#dbg_parameters
+def get_fig_params(disparity_ranges):
+    fig_params = []
+    for dr in disparity_ranges:
+        if dr[-1][0]=='-':
+            fig_params.append(None)
+        else:
+            subs = []
+            for s in dr[:-1]:
+                mm = s[:2]
+                try:
+                    lims = s[2]
+                except IndexError:
+                    lims = None
+                subs.append({'lim_val':mm, 'lim_xy':lims})        
+            fig_params.append({'name':dr[-1],'ranges':subs}) 
+    return fig_params
+
+#try:
+fig_params = get_fig_params(dbg_parameters['disparity_ranges'])
+
+pass
+figs = []
+def setlimsxy(lim_xy):
+    if not lim_xy is None:
+        plt.xlim(min(lim_xy[:2]),max(lim_xy[:2]))            
+        plt.ylim(max(lim_xy[2:]),min(lim_xy[2:]))            
+    
+for nfile, fpars in enumerate(fig_params):
+    if not fpars is None:
+        data = qsf.result_npy_prepare(files['result'][nfile], ABSOLUTE_DISPARITY, fix_nan=True, insert_deltas=True)
+        
+        for rng in fpars['ranges']:
+            lim_val = rng['lim_val']
+            lim_xy =  rng['lim_xy']
+            fig = plt.figure(figsize=FIGSIZE)
+            fig.canvas.set_window_title(fpars['name'])
+            fig.suptitle(fpars['name'])
+            ax_conf=plt.subplot(322)
+            ax_conf.set_title("Ground truth confidence")
+#            fig.suptitle("Groud truth confidence")
+            plt.imshow(data[...,GT_CONF], vmin=0, vmax=CONF_MAX, cmap='gray')
+            if not lim_xy is None:
+                pass # show frame
+                xdata=[min(lim_xy[:2]),max(lim_xy[:2]),max(lim_xy[:2]),min(lim_xy[:2]),min(lim_xy[:2])]
+                ydata=[min(lim_xy[2:]),min(lim_xy[2:]),max(lim_xy[2:]),max(lim_xy[2:]),min(lim_xy[2:])]
+                plt.plot(xdata,ydata,color=WOI_COLOR)
+            
+#            setlimsxy(lim_xy)
+            plt.colorbar(orientation='vertical') # location='bottom')
+            
+            ax_gtd=plt.subplot(321)
+            ax_gtd.set_title("Ground truth disparity map")
+            plt.imshow(data[...,GT_DISP], vmin=lim_val[0], vmax=lim_val[1])
+            setlimsxy(lim_xy)            
+            plt.colorbar(orientation='vertical') # location='bottom')
+            
+            ax_hed=plt.subplot(323)
+            ax_hed.set_title("Heuristic disparity map")
+            plt.imshow(data[...,HEUR_NAN], vmin=lim_val[0], vmax=lim_val[1])            
+            setlimsxy(lim_xy)                        
+            plt.colorbar(orientation='vertical') # location='bottom')
+        
+            ax_nnd=plt.subplot(325)
+            ax_nnd.set_title("Network disparity output")
+            plt.imshow(data[...,NN_NAN], vmin=lim_val[0], vmax=lim_val[1])
+            setlimsxy(lim_xy)                        
+            plt.colorbar(orientation='vertical') # location='bottom')
+
+            ax_hee=plt.subplot(324)
+            ax_hee.set_title("Heuristic disparity error")
+            plt.imshow(data[...,HEUR_DIFF], vmin=-ERR_AMPL, vmax=ERR_AMPL)            
+            setlimsxy(lim_xy)                        
+            plt.colorbar(orientation='vertical') # location='bottom')
+
+            ax_nne=plt.subplot(326)
+            ax_nne.set_title("Network disparity error")
+            plt.imshow(data[...,NN_DIFF], vmin=-ERR_AMPL, vmax=ERR_AMPL)            
+            setlimsxy(lim_xy)                        
+            plt.colorbar(orientation='vertical') # location='bottom')
+        
+            plt.tight_layout(rect =[0,0,1,TIGHT_TOP], h_pad = TIGHT_HPAD, w_pad = TIGHT_WPAD)
+            
+            figs.append(fig)
+            pass
+
+#whow to allow adjustment before applying tight_layout?
+pass
+for fig in figs:
+    fig.tight_layout(rect =[0,0,1,TIGHT_TOP], h_pad = TIGHT_HPAD, w_pad = TIGHT_WPAD)
+plt.show()
+
+
+
+#qsf.evaluateAllResults(result_files = files['result'],
+#                       absolute_disparity = ABSOLUTE_DISPARITY,
+#                       cluster_radius = CLUSTER_RADIUS)
+print("All done")
+exit (0)

qcstereo_functions.py

@@ -30,13 +30,14 @@ def print_time(txt="",end="\n"):
         txt +=" "
     print(("%s"+bcolors.BOLDWHITE+"at %.4fs (+%.4fs)"+bcolors.ENDC)%(txt,t-TIME_START,t-TIME_LAST), end = end, flush=True)
     TIME_LAST = t
+    
 def parseXmlConfig(conf_file, root_dir):
     tree = ET.parse(conf_file)
     root = tree.getroot()
     parameters = {}
     for p in root.find('parameters'):
         parameters[p.tag]=eval(p.text.strip())
-    globals    
+#    globals    
     dirs={}
     for p in root.find('directories'):
         dirs[p.tag]=eval(p.text.strip())
@@ -46,7 +47,11 @@ def parseXmlConfig(conf_file, root_dir):
     for p in root.find('files'):
         files[p.tag]=eval(p.text.strip())
 #    globals().update(parameters)
-    return parameters, dirs, files
+    dbg_parameters = {}
+    for p in root.find('dbg_parameters'):
+        dbg_parameters[p.tag]=eval(p.text.strip())
+
+    return parameters, dirs, files, dbg_parameters
 
 
 
@@ -84,7 +89,8 @@ def readTFRewcordsEpoch(train_filename):
     npy_dir_name = "npy"
     dirname = os.path.dirname(train_filename) 
     npy_dir = os.path.join(dirname, npy_dir_name)
-    filebasename, file_extension = os.path.splitext(train_filename)
+#    filebasename, file_extension = os.path.splitext(train_filename)
+    filebasename, _ = os.path.splitext(train_filename)
     filebasename = os.path.basename(filebasename)
     file_corr2d =           os.path.join(npy_dir,filebasename + '_corr2d.npy')
     file_target_disparity = os.path.join(npy_dir,filebasename + '_target_disparity.npy')
@@ -179,7 +185,7 @@ def add_neibs(npa_ext,radius):
     height = npa_ext.shape[0]-2*radius
     width =  npa_ext.shape[1]-2*radius
     side = 2 * radius + 1
-    size = side * side
+#    size = side * side
     npa_neib = np.empty((height,  width, side, side, npa_ext.shape[2]), dtype = npa_ext.dtype)
     for dy in range (side):
         for dx in range (side):
@@ -187,8 +193,8 @@ def add_neibs(npa_ext,radius):
     return npa_neib.reshape(height, width, -1)    
   
 def extend_img_to_clusters(datasets_img,radius, width): #  = 324):
-    side = 2 * radius + 1
-    size = side * side
+#    side = 2 * radius + 1
+#    size = side * side
     if len(datasets_img) ==0:
         return
     num_tiles = datasets_img[0]['corr2d'].shape[0]
@@ -210,7 +216,7 @@ def reformat_to_clusters(datasets_data, cluster_radius):
 
 def flip_horizontal(datasets_data, cluster_radius, tile_layers, tile_side):
     cluster_side = 2 * cluster_radius + 1
-    cluster_size = cluster_side * cluster_side
+#    cluster_size = cluster_side * cluster_side
     """
 TILE_LAYERS =        4
 TILE_SIDE =          9 # 7
@@ -238,8 +244,8 @@ TILE_SIZE =         TILE_SIDE* TILE_SIDE # == 81
         rec['target_disparity'] = target_disparity.reshape((target_disparity.shape[0],-1)) 
         rec['gt_ds'] =            gt_ds.reshape((gt_ds.shape[0],-1))
 
-def replace_nan(datasets_data, cluster_radius):
-    cluster_size = (2 * cluster_radius + 1) * (2 * cluster_radius + 1)
+def replace_nan(datasets_data): # , cluster_radius):
+#    cluster_size = (2 * cluster_radius + 1) * (2 * cluster_radius + 1)
 # Reformat input data
     for rec in datasets_data:
         if not rec is None:
@@ -259,7 +265,7 @@ def permute_to_swaps(perm):
         
 def shuffle_in_place(datasets_data, indx, period):
     swaps = permute_to_swaps(np.random.permutation(len(datasets_data)))
-    num_entries = datasets_data[0]['corr2d'].shape[0] // period
+#    num_entries = datasets_data[0]['corr2d'].shape[0] // period
     for swp in swaps:
         ds0 = datasets_data[swp[0]]
         ds1 = datasets_data[swp[1]]
@@ -279,9 +285,10 @@ def shuffle_chunks_in_place(datasets_data, tiles_groups_per_chunk):
     """
     Improve shuffling by preserving indices inside batches (0 <->0, ... 39 <->39 for 40 tile group batches)
     """
-    num_files = len(datasets_data)
+#    num_files = len(datasets_data)
     #chunks_per_file = datasets_data[0]['target_disparity']
-    for nf, ds in enumerate(datasets_data):
+#    for nf, ds in enumerate(datasets_data):
+    for ds in datasets_data:
         groups_per_file = ds['corr2d'].shape[0]
         chunks_per_file = groups_per_file//tiles_groups_per_chunk
         permut = np.random.permutation(chunks_per_file)
@@ -327,7 +334,8 @@ def zip_lvar_hvar(datasets_all_data, del_src = True):
                    'target_disparity': np.empty((recs[0]['target_disparity'].shape[0]*num_sets_to_combine,recs[0]['target_disparity'].shape[1]),dtype=np.float32),
                    'gt_ds':            np.empty((recs[0]['gt_ds'].shape[0]*num_sets_to_combine,           recs[0]['gt_ds'].shape[1]),dtype=np.float32)}
             
-            for nset, reci in enumerate(recs):
+#            for nset, reci in enumerate(recs):
+            for nset, _ in enumerate(recs):
                 rec['corr2d']          [nset::num_sets_to_combine] =  recs[nset]['corr2d'] 
                 rec['target_disparity'][nset::num_sets_to_combine] =  recs[nset]['target_disparity'] 
                 rec['gt_ds']           [nset::num_sets_to_combine] =  recs[nset]['gt_ds'] 
@@ -356,10 +364,10 @@ def initTrainTestData(
         max_files_per_group, # shuffling buffer for files
         two_trains,
         train_next):
-    datasets_train_lvar =  []
-    datasets_train_hvar =  []
-    datasets_train_lvar1 = []
-    datasets_train_hvar1 = []
+#    datasets_train_lvar =  []
+#    datasets_train_hvar =  []
+#    datasets_train_lvar1 = []
+#    datasets_train_hvar1 = []
     datasets_train_all = [[],[],[],[]]
     for n_train, f_train in enumerate(files['train']):
         if len(f_train) and ((n_train<2) or two_trains):
@@ -445,7 +453,8 @@ def readImageData(image_data,
              cluster_radius,
              width)
         if replace_nans:
-            replace_nan([image_data[indx]], cluster_radius)
+#            replace_nan([image_data[indx]], cluster_radius)
+            replace_nan([image_data[indx]])
             
     return image_data[indx]
                
@@ -477,7 +486,7 @@ def evaluateAllResults(result_files, absolute_disparity, cluster_radius):
     
 
 
-def result_npy_to_tiff(npy_path, absolute, fix_nan, insert_deltas=True):
+def result_npy_prepare(npy_path, absolute, fix_nan, insert_deltas=True):
     
     """
     @param npy_path full path to the npy file with 4-layer data (242,324,4) - nn_disparity(offset), target_disparity, gt disparity, gt strength
@@ -485,10 +494,9 @@ def result_npy_to_tiff(npy_path, absolute, fix_nan, insert_deltas=True):
     @param absolute - True - the first layer contains absolute disparity, False - difference from target_disparity
     @param fix_nan - replace nan in target_disparity with 0 to apply offset, target_disparity will still contain nan
     """
-    tiff_path = npy_path.replace('.npy','.tiff')
     data = np.load(npy_path) #(324,242,4) [nn_disp, target_disp,gt_disp, gt_conf]
     nn_out =            0
-    target_disparity =  1     
+#    target_disparity =  1     
     gt_disparity =      2     
     gt_strength =       3     
     if not absolute:
@@ -501,20 +509,28 @@ def result_npy_to_tiff(npy_path, absolute, fix_nan, insert_deltas=True):
         data = np.concatenate([data[...,0:4],data[...,0:2],data[...,0:2],data[...,4:]], axis = 2)
         data[...,6] -= data[...,gt_disparity] 
         data[...,7] -= data[...,gt_disparity]
-        for l in [4,5,6,7]:
+        for l in [2, 4, 5, 6, 7]:
             data[...,l] = np.select([data[...,gt_strength]==0.0, data[...,gt_strength]>0.0], [np.nan,data[...,l]])
         # All other layers - mast too
         for l in range(8,data.shape[2]):
             data[...,l] = np.select([data[...,gt_strength]==0.0, data[...,gt_strength]>0.0], [np.nan,data[...,l]])
-            
-#        data[...,4] = np.select([data[...,3]==0.0, data[...,3]>0.0], [np.nan,data[...,4]])
-#       data[...,5] = np.select([data[...,3]==0.0, data[...,3]>0.0], [np.nan,data[...,5]])
+    return data        
+
+def result_npy_to_tiff(npy_path, absolute, fix_nan, insert_deltas=True):
+    
+    """
+    @param npy_path full path to the npy file with 4-layer data (242,324,4) - nn_disparity(offset), target_disparity, gt disparity, gt strength
+           data will be written as 4-layer tiff, extension '.npy' replaced with '.tiff'
+    @param absolute - True - the first layer contains absolute disparity, False - difference from target_disparity
+    @param fix_nan - replace nan in target_disparity with 0 to apply offset, target_disparity will still contain nan
+    """
+    data = result_npy_prepare(npy_path, absolute, fix_nan, insert_deltas)
+    tiff_path = npy_path.replace('.npy','.tiff')
             
     data = data.transpose(2,0,1)
     print("Saving results to TIFF: "+tiff_path)
     imagej_tiffwriter.save(tiff_path,data[...,np.newaxis])        
 
-
 def eval_results(rslt_path, absolute,
                  min_disp =       -0.1, #minimal GT disparity
                  max_disp =       20.0, # maximal GT disparity

qcstereo_losses.py

@@ -4,7 +4,7 @@ __license__   = "GPL-3.0+"
 __email__     = "andrey@elphel.com"
 
 #from numpy import float64
-import numpy as np
+#import numpy as np
 import tensorflow as tf
 
 def smoothLoss(out_batch,                   # [batch_size,(1..2)] tf_result
@@ -76,7 +76,7 @@ def batchLoss(out_batch,                   # [batch_size,(1..2)] tf_result
               absolute_disparity =     False, #when false there should be no activation on disparity output ! 
               use_confidence =         False, 
               lambda_conf_avg =        0.01,
-              lambda_conf_pwr =        0.1,
+##              lambda_conf_pwr =        0.1,
               conf_pwr =               2.0,
               gt_conf_offset =         0.08,
               gt_conf_pwr =            1.0,
@@ -90,14 +90,14 @@ def batchLoss(out_batch,                   # [batch_size,(1..2)] tf_result
         Here confidence should be after relU. Disparity - may be also if absolute, but no activation if output is residual disparity
         """
         tf_lambda_conf_avg = tf.constant(lambda_conf_avg, dtype=tf.float32, name="tf_lambda_conf_avg")
-        tf_lambda_conf_pwr = tf.constant(lambda_conf_pwr, dtype=tf.float32, name="tf_lambda_conf_pwr")
-        tf_conf_pwr =        tf.constant(conf_pwr,        dtype=tf.float32, name="tf_conf_pwr")
+##        tf_lambda_conf_pwr = tf.constant(lambda_conf_pwr, dtype=tf.float32, name="tf_lambda_conf_pwr")
+##        tf_conf_pwr =        tf.constant(conf_pwr,        dtype=tf.float32, name="tf_conf_pwr")
         tf_gt_conf_offset =  tf.constant(gt_conf_offset,  dtype=tf.float32, name="tf_gt_conf_offset")
         tf_gt_conf_pwr =     tf.constant(gt_conf_pwr,     dtype=tf.float32, name="tf_gt_conf_pwr")
         tf_num_tiles =       tf.shape(gt_ds_batch)[0]
         tf_0f =              tf.constant(0.0,             dtype=tf.float32, name="tf_0f")
         tf_1f =              tf.constant(1.0,             dtype=tf.float32, name="tf_1f")
-        tf_maxw =            tf.constant(1.0,             dtype=tf.float32, name="tf_maxw")
+##        tf_maxw =            tf.constant(1.0,             dtype=tf.float32, name="tf_maxw")
         tf_disp_diff_cap2=   tf.constant(disp_diff_cap*disp_diff_cap,  dtype=tf.float32, name="disp_diff_cap2")
         tf_disp_diff_slope=  tf.constant(disp_diff_slope, dtype=tf.float32, name="disp_diff_slope")
         
@@ -197,7 +197,7 @@ def weightsLoss(inp_weights,
                 tile_side,
                 wborders_zero):
                 
-                       # [batch_size,(1..2)] tf_result
+                # [batch_size,(1..2)] tf_result
 #                weights_lambdas):  # single lambda or same length as inp_weights.shape[1]
     """
     Enforcing 'smooth' weights for the input 2d correlation tiles