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python3-imagej-tiff
Commit c1f82436 authored by Andrey Filippov's avatar Andrey Filippov
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Generating TFRecord files for multiple epochs and for multi-tile NN

parent d7fc8ac4
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Showing with 159 additions and 42 deletions
explore_data.py
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......@@ -268,7 +268,7 @@ class ExploreData:
#disp_thesh
disp_avar = disp_max - disp_min
disp_rvar = disp_avar * disp_thesh / disp_max
disp_rvar = disp_avar * disp_thesh / np.maximum(disp_max, 0.001) # removing division by 0 error - those tiles will be anyway discarded
disp_var = np.select([disp_max >= disp_thesh, disp_max < disp_thesh],[disp_rvar,disp_avar])
return disp_var, tile_neibs
......@@ -355,7 +355,7 @@ class ExploreData:
bb = np.empty_like(data_ds[...,0],dtype=int)
for findx in range(data_ds.shape[0]):
ds = data_ds[findx]
gt = ds[...,1] > 0.0 # all true - check
gt = ds[...,1] > 0.0 # OK
db = (((ds[...,0] - self.disparity_min_clip)/disp_step).astype(int))*gt
sb = (((ds[...,1] - self.strength_min_clip)/ str_step).astype(int))*gt
np.clip(db, 0, self.disparity_bins-1, out = db)
......@@ -395,16 +395,18 @@ class ExploreData:
for i in range (self.hist_to_batch.max()+1):
lst.append([])
# bb1d = bb[findx].reshape(self.num_tiles)
disp_var_tiles = disp_var[findx].reshape(self.num_tiles)
disp_neibs_tiles = disp_neibs[findx].reshape(self.num_tiles)
for n, indx in enumerate(bb[findx].reshape(self.num_tiles)):
if indx >= 0:
if use_neibs:
disp_var_tiles = disp_var[findx].reshape(self.num_tiles)
disp_neibs_tiles = disp_neibs[findx].reshape(self.num_tiles)
if disp_neibs_tiles[indx] < min_neibs:
# disp_var_tiles = disp_var[findx].reshape(self.num_tiles)
# disp_neibs_tiles = disp_neibs[findx].reshape(self.num_tiles)
if disp_neibs_tiles[n] < min_neibs:
continue # too few neighbors
if not disp_var_tiles[indx] >= min_var:
if not disp_var_tiles[n] >= min_var:
continue #too small variance
if not disp_var_tiles[indx] < max_var:
if not disp_var_tiles[n] < max_var:
continue #too large variance
lst[indx].append(foffs + n)
lst_arr=[]
......@@ -473,7 +475,7 @@ class ExploreData:
for fn in flist:
ml_patt = os.path.join(os.path.dirname(fn), ExploreData.ML_DIR, ExploreData.ML_PATTERN)
ml_list.append(glob.glob(ml_patt))
self.ml_list = ml_list
## self.ml_list = ml_list
return ml_list
def getBatchData(
......@@ -501,18 +503,26 @@ class ExploreData:
return ml_all_files
def prepareBatchData(self, seed_index, min_choices=None, max_files = None, ml_num = None, test_set = False):
def prepareBatchData(self, ml_list, seed_index, min_choices=None, max_files = None, ml_num = None, set_ds = None, radius = 0):
if min_choices is None:
min_choices = self.min_batch_choices
if max_files is None:
max_files = self.max_batch_files
if ml_num is None:
ml_num = self.files_per_scene
set_ds = [self.train_ds, self.test_ds][test_set]
if set_ds is None:
set_ds = self.train_ds
tiles_in_sample = (2 * radius + 1) * (2 * radius + 1)
height = set_ds.shape[1]
width = set_ds.shape[2]
width_m1 = width-1
height_m1 = height-1
# set_ds = [self.train_ds, self.test_ds][test_set]
corr_layers = ['hor-pairs', 'vert-pairs','diagm-pair', 'diago-pair']
flist,tiles = self.augmentBatchFileIndices(seed_index, min_choices, max_files, set_ds)
ml_all_files = self.getBatchData(flist, tiles, self.ml_list, ml_num) # 0 - use all ml files for the scene, >0 select random number
# ml_all_files = self.getBatchData(flist, tiles, self.ml_list, ml_num) # 0 - use all ml files for the scene, >0 select random number
ml_all_files = self.getBatchData(flist, tiles, ml_list, ml_num) # 0 - use all ml files for the scene, >0 select random number
if self.debug_level > 1:
print ("==============",seed_index, flist)
for i, findx in enumerate(flist):
......@@ -524,19 +534,35 @@ class ExploreData:
if self.debug_level > 1:
print("Tiles in the batch=",total_tiles)
corr2d_batch = None # np.empty((total_tiles, len(corr_layers),81))
gt_ds_batch = np.empty((total_tiles,2), dtype=float)
target_disparity_batch = np.empty((total_tiles,), dtype=float)
gt_ds_batch = np.empty((total_tiles * tiles_in_sample, 2), dtype=float)
target_disparity_batch = np.empty((total_tiles * tiles_in_sample, ), dtype=float)
start_tile = 0
for nscene, scene_files in enumerate(ml_all_files):
for path in scene_files:
img = ijt.imagej_tiff(path, corr_layers, tile_list=tiles[nscene])
'''
Create tiles list including neighbors
'''
full_tiles = np.empty([len(tiles[nscene]) * tiles_in_sample], dtype = int)
indx = 0;
for i, nt in enumerate(tiles[nscene]):
ty = nt // width
tx = nt % width
for dy in range (-radius, radius+1):
y = np.clip(ty+dy,0,height_m1)
for dx in range (-radius, radius+1):
x = np.clip(tx+dx,0,width_m1)
full_tiles[indx] = y * width + x
indx += 1
#now tile_list is np.array instead of the list, but it seems to be OK
img = ijt.imagej_tiff(path, corr_layers, tile_list=full_tiles) # tiles[nscene])
corr2d = img.corr2d
target_disparity = img.target_disparity
gt_ds = img.gt_ds
end_tile = start_tile + corr2d.shape[0]
if corr2d_batch is None:
corr2d_batch = np.empty((total_tiles, len(corr_layers), corr2d.shape[-1]))
# corr2d_batch = np.empty((total_tiles, tiles_in_sample * len(corr_layers), corr2d.shape[-1]))
corr2d_batch = np.empty((total_tiles * tiles_in_sample, len(corr_layers), corr2d.shape[-1]))
gt_ds_batch [start_tile:end_tile] = gt_ds
target_disparity_batch [start_tile:end_tile] = target_disparity
corr2d_batch [start_tile:end_tile] = corr2d
......@@ -564,17 +590,24 @@ class ExploreData:
self.gt_ds_batch = gt_ds_batch
return corr2d_batch, target_disparity_batch, gt_ds_batch
def writeTFRewcordsEpoch(self, tfr_filename, test_set=False):
def writeTFRewcordsEpoch(self, tfr_filename, ml_list, files_list = None, set_ds= None, radius = 0): # test_set=False):
# train_filename = 'train.tfrecords' # address to save the TFRecords file
# open the TFRecords file
if not '.tfrecords' in tfr_filename:
tfr_filename += '.tfrecords'
if files_list is None:
files_list = self.files_train
if set_ds is None:
set_ds = self.train_ds
writer = tf.python_io.TFRecordWriter(tfr_filename)
files_list = [self.files_train, self.files_test][test_set]
#$ files_list = [self.files_train, self.files_test][test_set]
seed_list = np.arange(len(files_list))
np.random.shuffle(seed_list)
for nscene, seed_index in enumerate(seed_list):
corr2d_batch, target_disparity_batch, gt_ds_batch = ex_data.prepareBatchData(seed_index, min_choices=None, max_files = None, ml_num = None, test_set = test_set)
corr2d_batch, target_disparity_batch, gt_ds_batch = ex_data.prepareBatchData(ml_list, seed_index, min_choices=None, max_files = None, ml_num = None, set_ds = set_ds, radius = radius)
#shuffles tiles in a batch
tiles_in_batch = len(target_disparity_batch)
permut = np.random.permutation(tiles_in_batch)
......@@ -586,6 +619,7 @@ class ExploreData:
dtype_target_disparity = _dtype_feature(target_disparity_batch_shuffled)
dtype_feature_gt_ds = _dtype_feature(gt_ds_batch_shuffled)
for i in range(tiles_in_batch):
x = corr2d_batch_shuffled[i].astype(np.float32)
y = target_disparity_batch_shuffled[i].astype(np.float32)
z = gt_ds_batch_shuffled[i].astype(np.float32)
......@@ -638,8 +672,8 @@ class ExploreData:
good_tiles[ids] &= variance < variance_max
disparity = np.nan_to_num(disparity, copy = False) # to be able to multiply by 0.0 in mask | copy=False, then out=disparity all done in-place
strength = np.nan_to_num(strength, copy = False) # likely should never happen
np.clip(disparity, self.disparity_min_clip, self.disparity_max_clip, out = disparity)
np.clip(strength, self.strength_min_clip, self.strength_max_clip, out = strength)
# np.clip(disparity, self.disparity_min_clip, self.disparity_max_clip, out = disparity)
# np.clip(strength, self.strength_min_clip, self.strength_max_clip, out = strength)
good_tiles_list.append(good_tiles)
combo_rds = np.concatenate(rds_list)
hist, xedges, yedges = np.histogram2d( # xedges, yedges - just for debugging
......@@ -675,21 +709,30 @@ if __name__ == "__main__":
topdir_test = "/mnt/dde6f983-d149-435e-b4a2-88749245cc6c/home/eyesis/x3d_data/data_sets/test"#test" #all/"
try:
train_filenameTFR = sys.argv[3]
except IndexError:
train_filenameTFR = "/mnt/dde6f983-d149-435e-b4a2-88749245cc6c/home/eyesis/x3d_data/data_sets/tf_data/train_01.tfrecords"
try:
test_filenameTFR = sys.argv[4]
pathTFR = sys.argv[3]
except IndexError:
test_filenameTFR = "/mnt/dde6f983-d149-435e-b4a2-88749245cc6c/home/eyesis/x3d_data/data_sets/tf_data/test_01.tfrecords"
pathTFR = "/mnt/dde6f983-d149-435e-b4a2-88749245cc6c/home/eyesis/x3d_data/data_sets/tf_data/tf"
#Parameters to generate neighbors data. Set radius to 0 to generate single-tile
RADIUS = 1
MIN_NEIBS = (2 * RADIUS + 1) * (2 * RADIUS + 1) # All tiles valid
MIN_NEIBS = (2 * RADIUS + 1) * (2 * RADIUS + 1) # All tiles valid == 9
VARIANCE_THRESHOLD = 1.5
NUM_TRAIN_SETS = 2
if RADIUS == 0:
BATCH_DISP_BINS = 20
BATCH_STR_BINS = 10
else:
BATCH_DISP_BINS = 8
BATCH_STR_BINS = 3
train_filenameTFR = pathTFR+"-train"
test_filenameTFR = pathTFR+"-test"
# disp_bins = 20,
# str_bins=10)
# corr2d, target_disparity, gt_ds = readTFRewcordsEpoch(train_filenameTFR)
# print_time("Read %d tiles"%(corr2d.shape[0]))
# exit (0)
# exit (0)
ex_data = ExploreData(
topdir_train = topdir_train,
topdir_test = topdir_test,
......@@ -715,8 +758,8 @@ if __name__ == "__main__":
plt.imshow(ex_data.blurred_hist, vmin=0, vmax=.1 * ex_data.blurred_hist.max())#,vmin=-6,vmax=-2) # , vmin=0, vmax=.01)
plt.colorbar(orientation='horizontal') # location='bottom')
hist_to_batch = ex_data.assignBatchBins(
disp_bins = 20,
str_bins=10)
disp_bins = BATCH_DISP_BINS,
str_bins = BATCH_STR_BINS)
bb_display = hist_to_batch.copy()
bb_display = ( 1+ (bb_display % 2) + 2 * ((bb_display % 20)//10)) * (hist_to_batch > 0) #).astype(float)
fig2 = plt.figure()
......@@ -732,7 +775,10 @@ if __name__ == "__main__":
if (RADIUS > 0):
disp_var_test, num_neibs_test = ex_data.exploreNeibs(ex_data.test_ds, RADIUS)
disp_var_train, num_neibs_train = ex_data.exploreNeibs(ex_data.train_ds, RADIUS)
for var_thresh in [0.1, 1.0, 1.5, 2.0, 5.0]:
# show varinace histogram
# for var_thresh in [0.1, 1.0, 1.5, 2.0, 5.0]:
for var_thresh in [1.5]:
ex_data.showVariance(
rds_list = [ex_data.train_ds, ex_data.test_ds], # list of disparity/strength files, suchas training, testing
disp_var_list = [disp_var_train, disp_var_test], # list of disparity variance files. Same shape(but last dim) as rds_list
......@@ -749,22 +795,93 @@ if __name__ == "__main__":
neibs_min = 9)
pass
pass
# show varinace histogram
else:
disp_var_test, num_neibs_test = None, None
disp_var_train, num_neibs_train = None, None
ml_list=ex_data.getMLList(ex_data.files_test)
ex_data.makeBatchLists(data_ds = ex_data.test_ds)
ex_data.writeTFRewcordsEpoch(test_filenameTFR, test_set=True)
ml_list_train=ex_data.getMLList(ex_data.files_train)
ml_list_test= ex_data.getMLList(ex_data.files_test)
if RADIUS == 0 :
list_of_file_lists_train, num_batch_tiles_train = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.train_ds,
disp_var = disp_var_train, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_train, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = 0.0, # Minimal tile variance to include
max_var = VARIANCE_THRESHOLD, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
pass
# ex_data.makeBatchLists(data_ds = ex_data.train_ds)
for train_var in range (NUM_TRAIN_SETS):
fpath = train_filenameTFR+("-%03d"%(train_var,))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_train, files_list = ex_data.files_train, set_ds= ex_data.train_ds)
list_of_file_lists_test, num_batch_tiles_test = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.test_ds,
disp_var = disp_var_test, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_test, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = 0.0, # Minimal tile variance to include
max_var = VARIANCE_THRESHOLD, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
fpath = test_filenameTFR # +("-%03d"%(train_var,))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_train, files_list = ex_data.files_test, set_ds= ex_data.test_ds)
pass
else: # RADIUS > 0
# train
list_of_file_lists_train, num_batch_tiles_train = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.train_ds,
disp_var = disp_var_train, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_train, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = 0.0, # Minimal tile variance to include
max_var = VARIANCE_THRESHOLD, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
num_le_train = num_batch_tiles_train.sum()
print("Number of <= %f disparity variance tiles: %d (train)"%(VARIANCE_THRESHOLD, num_le_train))
for train_var in range (NUM_TRAIN_SETS):
fpath = train_filenameTFR+("-%03d_R%d_LE%4.1f"%(train_var,RADIUS,VARIANCE_THRESHOLD))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_train, files_list = ex_data.files_train, set_ds= ex_data.train_ds, radius = RADIUS)
""" prepare train dataset """
ml_list=ex_data.getMLList(ex_data.files_train) # train_list)
ex_data.makeBatchLists(data_ds = ex_data.train_ds)
ex_data.writeTFRewcordsEpoch(train_filenameTFR,test_set = False)
list_of_file_lists_train, num_batch_tiles_train = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.train_ds,
disp_var = disp_var_train, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_train, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = VARIANCE_THRESHOLD, # Minimal tile variance to include
max_var = 1000.0, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
num_gt_train = num_batch_tiles_train.sum()
high_fract_train = 1.0 * num_gt_train / (num_le_train + num_gt_train)
print("Number of > %f disparity variance tiles: %d, fraction = %f (train)"%(VARIANCE_THRESHOLD, num_gt_train, high_fract_train))
for train_var in range (NUM_TRAIN_SETS):
fpath = train_filenameTFR+("-%03d_R%d_GT%4.1f"%(train_var,RADIUS,VARIANCE_THRESHOLD))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_train, files_list = ex_data.files_train, set_ds= ex_data.train_ds, radius = RADIUS)
# test
list_of_file_lists_test, num_batch_tiles_test = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.test_ds,
disp_var = disp_var_test, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_test, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = 0.0, # Minimal tile variance to include
max_var = VARIANCE_THRESHOLD, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
num_le_test = num_batch_tiles_test.sum()
print("Number of <= %f disparity variance tiles: %d (est)"%(VARIANCE_THRESHOLD, num_le_test))
fpath = test_filenameTFR +("-TEST_R%d_LE%4.1f"%(RADIUS,VARIANCE_THRESHOLD))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_test, files_list = ex_data.files_test, set_ds= ex_data.test_ds, radius = RADIUS)
list_of_file_lists_test, num_batch_tiles_test = ex_data.makeBatchLists( # results are also saved to self.*
data_ds = ex_data.test_ds,
disp_var = disp_var_test, # difference between maximal and minimal disparity for each scene, each tile
disp_neibs = num_neibs_test, # number of valid tiles around each center tile (for 3x3 (radius = 1) - macximal is 9
min_var = VARIANCE_THRESHOLD, # Minimal tile variance to include
max_var = 1000.0, # Maximal tile variance to include
min_neibs = MIN_NEIBS) # Minimal number of valid tiles to include
num_gt_test = num_batch_tiles_test.sum()
high_fract_test = 1.0 * num_gt_test / (num_le_test + num_gt_test)
print("Number of > %f disparity variance tiles: %d, fraction = %f (test)"%(VARIANCE_THRESHOLD, num_gt_test, high_fract_test))
fpath = test_filenameTFR +("-TEST_R%d_GT%4.1f"%(RADIUS,VARIANCE_THRESHOLD))
ex_data.writeTFRewcordsEpoch(fpath, ml_list = ml_list_test, files_list = ex_data.files_test, set_ds= ex_data.test_ds, radius = RADIUS)
plt.show()
pass
......
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