Skip to content
Projects
Groups
Snippets
Help
Loading...
Help
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
P
python3-imagej-tiff
Project
Project
Details
Activity
Releases
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
Issues
0
Issues
0
List
Board
Labels
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Charts
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Elphel
python3-imagej-tiff
Commits
d786da7b
Commit
d786da7b
authored
Dec 01, 2021
by
Andrey Filippov
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
commited old modified files
parent
8ba9b224
Pipeline
#2436
failed with stages
Changes
4
Pipelines
1
Expand all
Show whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
1574 additions
and
72 deletions
+1574
-72
explore_data5m.py
explore_data5m.py
+1253
-0
imagej_tiffwriter.py
imagej_tiffwriter.py
+53
-53
nn_eval_01.py
nn_eval_01.py
+189
-9
qcstereo_functions.py
qcstereo_functions.py
+79
-10
No files found.
explore_data5m.py
0 → 100644
View file @
d786da7b
This diff is collapsed.
Click to expand it.
imagej_tiffwriter.py
View file @
d786da7b
nn_eval_01.py
View file @
d786da7b
This diff is collapsed.
Click to expand it.
qcstereo_functions.py
View file @
d786da7b
...
...
@@ -31,14 +31,14 @@ def print_time(txt="",end="\n"):
TIME_LAST
=
t
DEFAULT_TITLES
=
[
[
'test_lvar'
,
'Test_flat_heuristic'
],
[
'test_hvar'
,
'Test_edge_heuristic'
],
[
'test_lvar1'
,
'Test_flat_random'
],
[
'test_hvar1'
,
'Test_edge_random'
],
[
'fake_lvar'
,
'Fake_flat_heuristic'
],
[
'fake_hvar'
,
'Fake_edge_heuristic'
],
[
'fake_lvar1'
,
'Fake_flat_random'
],
[
'fake_hvar1'
,
'Fake_edge_random'
]]
[
'test_lvar'
,
'Test_flat_heuristic'
],
[
'test_hvar'
,
'Test_edge_heuristic'
],
[
'test_lvar1'
,
'Test_flat_random'
],
[
'test_hvar1'
,
'Test_edge_random'
],
[
'fake_lvar'
,
'Fake_flat_heuristic'
],
[
'fake_hvar'
,
'Fake_edge_heuristic'
],
[
'fake_lvar1'
,
'Fake_flat_random'
],
[
'fake_hvar1'
,
'Fake_edge_random'
]]
def
parseXmlConfig
(
conf_file
,
root_dir
):
tree
=
ET
.
parse
(
conf_file
)
...
...
@@ -517,6 +517,7 @@ def result_npy_prepare(npy_path, absolute, fix_nan, insert_deltas=True,labels=No
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
@parame insert_deltas: +1 - add delta layers, +2 - add variance (max - min of this and 8 neighbors)
"""
data
=
np
.
load
(
npy_path
)
#(324,242,4) [nn_disp, target_disp,gt_disp, gt_conf]
if
labels
is
None
:
...
...
@@ -526,12 +527,17 @@ def result_npy_prepare(npy_path, absolute, fix_nan, insert_deltas=True,labels=No
# target_disparity = 1
gt_disparity
=
2
gt_strength
=
3
heur_err
=
7
min_heur_err
=
0.001
height
=
data
.
shape
[
0
]
width
=
data
.
shape
[
1
]
nocenter9
=
np
.
array
([[[
1
,
1
,
1
,
1
,
np
.
nan
,
1
,
1
,
1
,
1
]]],
dtype
=
data
.
dtype
)
if
not
absolute
:
if
fix_nan
:
data
[
...
,
nn_out
]
+=
np
.
nan_to_num
(
data
[
...
,
1
],
copy
=
True
)
else
:
data
[
...
,
nn_out
]
+=
data
[
...
,
1
]
if
insert_deltas
:
if
(
insert_deltas
&
1
)
:
np
.
nan_to_num
(
data
[
...
,
gt_strength
],
copy
=
False
)
data
=
np
.
concatenate
([
data
[
...
,
0
:
4
],
data
[
...
,
0
:
2
],
data
[
...
,
0
:
2
],
data
[
...
,
4
:]],
axis
=
2
)
# data[...,4:] may be empty
labels
=
labels
[:
4
]
+
[
"nn_out"
,
"hier_out"
,
"nn_err"
,
"hier_err"
]
+
labels
[
4
:]
...
...
@@ -543,6 +549,69 @@ def result_npy_prepare(npy_path, absolute, fix_nan, insert_deltas=True,labels=No
# 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
]])
"""
Calculate bad tiles where ggt was used as a master, to remove them from the results (later versions add random error)
"""
bad1
=
abs
(
data
[
...
,
heur_err
])
<
min_heur_err
bad1_ext
=
np
.
concatenate
([
bad1
[
0
:
1
,:],
bad1
[
0
:
1
,:],
bad1
[:,:],
bad1
[
-
1
:
height
,:],
bad1
[
-
1
:
height
,:]],
axis
=
0
)
bad1_ext
=
np
.
concatenate
([
bad1_ext
[:,
0
:
1
],
bad1_ext
[:,
0
:
1
],
bad1_ext
[:,:],
bad1_ext
[:,
-
1
:
width
],
bad1_ext
[:,
-
1
:
width
]],
axis
=
1
)
bad25
=
np
.
empty
(
shape
=
[
height
,
width
,
25
],
dtype
=
bad1
.
dtype
)
bm25
=
np
.
array
([[[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
]]])
bm09
=
np
.
array
([[[
0
,
0
,
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
,
0
,
0
]]])
bm01
=
np
.
array
([[[
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
1
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
,
0
]]])
for
row
in
range
(
5
):
for
col
in
range
(
5
):
pass
bad25
[
...
,
row
*
5
+
col
]
=
bad1_ext
[
row
:
height
+
row
,
col
:
width
+
col
]
bad_num1
=
(
np
.
sum
(
bad25
*
bm25
,
axis
=
2
)
>
0
)
.
astype
(
data
.
dtype
)
bad_num2
=
(
np
.
sum
(
bad25
*
bm09
,
axis
=
2
)
>
0
)
.
astype
(
data
.
dtype
)
bad_num3
=
(
np
.
sum
(
bad25
*
bm01
,
axis
=
2
)
>
0
)
.
astype
(
data
.
dtype
)
bad_num
=
bad_num1
+
bad_num2
+
bad_num3
if
(
insert_deltas
&
2
):
wo
=
0.7
# ortho
wc
=
0.5
#corner
w8
=
np
.
array
([
wc
,
wo
,
wc
,
wo
,
0.0
,
wo
,
wc
,
wo
,
wc
],
dtype
=
data
.
dtype
)
w8
/=
np
.
sum
(
w8
)
#normalize
gt_ext
=
np
.
concatenate
([
data
[
0
:
1
,:,
gt_disparity
],
data
[:,:,
gt_disparity
],
data
[
-
1
:
height
,:,
gt_disparity
]],
axis
=
0
)
gt_ext
=
np
.
concatenate
([
gt_ext
[:,
0
:
1
],
gt_ext
[:,:],
gt_ext
[:,
-
1
:
width
]],
axis
=
1
)
gs_ext
=
np
.
concatenate
([
data
[
0
:
1
,:,
gt_strength
],
data
[:,:,
gt_strength
],
data
[
-
1
:
height
,:,
gt_strength
]],
axis
=
0
)
gs_ext
=
np
.
concatenate
([
gs_ext
[:,
0
:
1
],
gs_ext
[:,:],
gs_ext
[:,
-
1
:
width
]],
axis
=
1
)
data9
=
np
.
empty
(
shape
=
[
height
,
width
,
9
],
dtype
=
data
.
dtype
)
weight9
=
np
.
empty
(
shape
=
[
height
,
width
,
9
],
dtype
=
data
.
dtype
)
for
row
in
range
(
3
):
for
col
in
range
(
3
):
pass
data9
[
...
,
row
*
3
+
col
]
=
gt_ext
[
row
:
height
+
row
,
col
:
width
+
col
]
weight9
[
...
,
row
*
3
+
col
]
=
gs_ext
[
row
:
height
+
row
,
col
:
width
+
col
]
data9
*=
weight9
/
weight9
# make data=nan where wigth is 0
# data = np.concatenate([data[...],np.empty_like(data[...,-1])], axis = 2) # data[...,4:] may be empty
data
=
np
.
concatenate
([
data
[
...
],
np
.
empty
(
shape
=
[
height
,
width
,
4
],
dtype
=
data
.
dtype
)],
axis
=
2
)
# data[...,4:] may be empty
data
[
...
,
-
4
]
=
np
.
nanmax
(
data9
*
nocenter9
,
axis
=
2
)
-
np
.
nanmin
(
data9
*
nocenter9
,
axis
=
2
)
# will ignore nan
np
.
nan_to_num
(
data9
,
copy
=
False
)
# replace all nan in data9 with 0.
weight9
*=
w8
w_center
=
np
.
sum
(
weight9
,
axis
=
2
)
dw_center
=
np
.
sum
(
data9
*
weight9
,
axis
=
2
)
dw_center
/=
w_center
# now dw_center - weighted average in the center
data
[
...
,
-
3
]
=
np
.
abs
(
data
[
...
,
gt_disparity
]
-
dw_center
)
# data[...,-2] = data[...,gt_disparity]- dw_center
#data[...,-3] *= (data[...,-4] < 1.0) # just temporary
#data[...,-3] *= (data[...,gt_disparity] < 5) #just temporary
data
[
...
,
-
2
]
=
bad_num
.
astype
(
data
.
dtype
)
data
[
...
,
-
1
]
=
np
.
sum
(
np
.
nan_to_num
(
weight9
/
weight9
),
axis
=
2
)
.
astype
(
data
.
dtype
)
# data[...,-1] = dw_center
labels
+=
[
"max-min"
,
"abs-center"
,
"badness"
,
"neibs"
]
#neib = np.concatenate([gt_ext[:height,:width,:],],axis = )
pass
return
data
,
labels
def
result_npy_to_tiff
(
npy_path
,
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment