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QIM
Tools
qim3d
Commits
2fd4fae7
Commit
2fd4fae7
authored
1 year ago
by
s204159
Committed by
fima
1 year ago
Browse files
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Conv zarr nifti
parent
d2408c65
Branches
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Tags
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1 merge request
!100
Conv zarr nifti
Changes
2
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2 changed files
qim3d/io/convert.py
+78
-19
78 additions, 19 deletions
qim3d/io/convert.py
qim3d/utils/cli.py
+3
-0
3 additions, 0 deletions
qim3d/utils/cli.py
with
81 additions
and
19 deletions
qim3d/io/convert.py
+
78
−
19
View file @
2fd4fae7
...
...
@@ -2,16 +2,17 @@ import difflib
import
os
from
itertools
import
product
import
nibabel
as
nib
import
numpy
as
np
import
tifffile
as
tiff
import
zarr
from
tqdm
import
tqdm
from
qim3d.utils.internal_tools
import
stringify_path
from
qim3d.io.saving
import
save
class
Convert
:
def
__init__
(
self
,
**
kwargs
):
"""
Utility class to convert files to other formats without loading the entire file into memory
...
...
@@ -20,18 +21,25 @@ class Convert:
"""
self
.
chunk_shape
=
kwargs
.
get
(
"
chunk_shape
"
,
(
64
,
64
,
64
))
def
convert
(
self
,
input_path
,
output_path
):
def
get_file_extension
(
file_path
):
root
,
ext
=
os
.
path
.
splitext
(
file_path
)
if
ext
in
[
'
.gz
'
,
'
.bz2
'
,
'
.xz
'
]:
# handle common compressed extensions
root
,
ext2
=
os
.
path
.
splitext
(
root
)
ext
=
ext2
+
ext
return
ext
# Stringify path in case it is not already a string
input_path
=
stringify_path
(
input_path
)
input_ext
=
os
.
path
.
splitext
(
input_path
)
[
1
]
output_ext
=
os
.
path
.
splitext
(
output_path
)
[
1
]
input_ext
=
get_file_extension
(
input_path
)
output_ext
=
get_file_extension
(
output_path
)
output_path
=
stringify_path
(
output_path
)
if
os
.
path
.
isfile
(
input_path
):
match
input_ext
,
output_ext
:
case
(
"
.tif
"
,
"
.zarr
"
)
|
(
"
.tiff
"
,
"
.zarr
"
):
return
self
.
convert_tif_to_zarr
(
input_path
,
output_path
,
chunks
=
self
.
chunk_shape
)
return
self
.
convert_tif_to_zarr
(
input_path
,
output_path
)
case
(
"
.nii
"
,
"
.zarr
"
)
|
(
"
.nii.gz
"
,
"
.zarr
"
):
return
self
.
convert_nifti_to_zarr
(
input_path
,
output_path
)
case
_
:
raise
ValueError
(
"
Unsupported file format
"
)
# Load a directory
...
...
@@ -39,6 +47,10 @@ class Convert:
match
input_ext
,
output_ext
:
case
(
"
.zarr
"
,
"
.tif
"
)
|
(
"
.zarr
"
,
"
.tiff
"
):
return
self
.
convert_zarr_to_tif
(
input_path
,
output_path
)
case
(
"
.zarr
"
,
"
.nii
"
):
return
self
.
convert_zarr_to_nifti
(
input_path
,
output_path
)
case
(
"
.zarr
"
,
"
.nii.gz
"
):
return
self
.
convert_zarr_to_nifti
(
input_path
,
output_path
,
compression
=
True
)
case
_
:
raise
ValueError
(
"
Unsupported file format
"
)
# Fail
...
...
@@ -55,7 +67,7 @@ class Convert:
else
:
raise
ValueError
(
"
Invalid path
"
)
def
convert_tif_to_zarr
(
self
,
tif_path
,
zarr_path
,
chunks
=
(
64
,
64
,
64
)
):
def
convert_tif_to_zarr
(
self
,
tif_path
,
zarr_path
):
"""
Convert a tiff file to a zarr file
Args:
...
...
@@ -67,12 +79,18 @@ class Convert:
zarr.core.Array: zarr array containing the data from the tiff file
"""
vol
=
tiff
.
memmap
(
tif_path
)
z
=
zarr
.
open
(
zarr_path
,
mode
=
'
w
'
,
shape
=
vol
.
shape
,
chunks
=
chunks
,
dtype
=
vol
.
dtype
)
z
=
zarr
.
open
(
zarr_path
,
mode
=
"
w
"
,
shape
=
vol
.
shape
,
chunks
=
self
.
chunk_shape
,
dtype
=
vol
.
dtype
)
chunk_shape
=
tuple
((
s
+
c
-
1
)
//
c
for
s
,
c
in
zip
(
z
.
shape
,
z
.
chunks
))
# ! Fastest way is z[:] = vol[:], but does not have a progress bar
for
chunk_indices
in
tqdm
(
product
(
*
[
range
(
n
)
for
n
in
chunk_shape
]),
total
=
np
.
prod
(
chunk_shape
)):
slices
=
tuple
(
slice
(
c
*
i
,
min
(
c
*
(
i
+
1
),
s
))
for
s
,
c
,
i
in
zip
(
z
.
shape
,
z
.
chunks
,
chunk_indices
))
for
chunk_indices
in
tqdm
(
product
(
*
[
range
(
n
)
for
n
in
chunk_shape
]),
total
=
np
.
prod
(
chunk_shape
)
):
slices
=
tuple
(
slice
(
c
*
i
,
min
(
c
*
(
i
+
1
),
s
))
for
s
,
c
,
i
in
zip
(
z
.
shape
,
z
.
chunks
,
chunk_indices
)
)
temp_data
=
vol
[
slices
]
# The assignment takes 99% of the cpu-time
z
.
blocks
[
chunk_indices
]
=
temp_data
...
...
@@ -90,7 +108,49 @@ class Convert:
None
"""
z
=
zarr
.
open
(
zarr_path
)
tiff
.
imwrite
(
tif_path
,
z
)
save
(
tif_path
,
z
)
def
convert_nifti_to_zarr
(
self
,
nifti_path
,
zarr_path
):
"""
Convert a nifti file to a zarr file
Args:
nifti_path (str): path to the nifti file
zarr_path (str): path to the zarr file
Returns:
zarr.core.Array: zarr array containing the data from the nifti file
"""
vol
=
nib
.
load
(
nifti_path
).
dataobj
z
=
zarr
.
open
(
zarr_path
,
mode
=
"
w
"
,
shape
=
vol
.
shape
,
chunks
=
self
.
chunk_shape
,
dtype
=
vol
.
dtype
)
chunk_shape
=
tuple
((
s
+
c
-
1
)
//
c
for
s
,
c
in
zip
(
z
.
shape
,
z
.
chunks
))
# ! Fastest way is z[:] = vol[:], but does not have a progress bar
for
chunk_indices
in
tqdm
(
product
(
*
[
range
(
n
)
for
n
in
chunk_shape
]),
total
=
np
.
prod
(
chunk_shape
)
):
slices
=
tuple
(
slice
(
c
*
i
,
min
(
c
*
(
i
+
1
),
s
))
for
s
,
c
,
i
in
zip
(
z
.
shape
,
z
.
chunks
,
chunk_indices
)
)
temp_data
=
vol
[
slices
]
# The assignment takes 99% of the cpu-time
z
.
blocks
[
chunk_indices
]
=
temp_data
return
z
def
convert_zarr_to_nifti
(
self
,
zarr_path
,
nifti_path
,
compression
=
False
):
"""
Convert a zarr file to a nifti file
Args:
zarr_path (str): path to the zarr file
nifti_path (str): path to the nifti file
Returns:
None
"""
z
=
zarr
.
open
(
zarr_path
)
save
(
nifti_path
,
z
,
compression
=
compression
)
def
convert
(
input_path
:
str
,
output_path
:
str
,
chunk_shape
:
tuple
=
(
64
,
64
,
64
)):
...
...
@@ -101,6 +161,5 @@ def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)
output_path (str): path to the output file
chunk_shape (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
"""
converter
=
Convert
(
chunk_shape
=
chunk_shape
)
converter
.
convert
(
input_path
,
output_path
)
This diff is collapsed.
Click to expand it.
qim3d/utils/cli.py
+
3
−
0
View file @
2fd4fae7
...
...
@@ -189,6 +189,9 @@ def main():
parser
.
print_help
()
print
(
"
\n
"
)
elif
args
.
subcommand
==
'
convert
'
:
qim3d
.
io
.
convert
(
args
.
input_path
,
args
.
output_path
)
if
__name__
==
"
__main__
"
:
main
()
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