Refactor stitch-align code into align package

lens-biophotonics · Jan 25, 2021 · a0b6865 · a0b6865
1 parent 3f8aafb
commit a0b6865
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Showing 12 changed files with 13 additions and 13 deletions.
diff --git a/zetastitcher/__main__.py → scripts/align_debug.py b/zetastitcher/__main__.py → scripts/align_debug.py
@@ -8,7 +8,7 @@
 
 import cv2 as cv
 
-from .io.inputfile import InputFile
+from zetastitcher.io.inputfile import InputFile
 
 
 def to_dtype(x, dtype):

diff --git a/setup.py b/setup.py
@@ -94,7 +94,7 @@
     # pip to create the appropriate form of executable for the target platform.
     entry_points={
         'console_scripts': [
-            'stitch-align = zetastitcher.runner:main',
+            'stitch-align = zetastitcher.align.__main__:main',
             'stitch-fuse = zetastitcher.fuse.__main__:main',
             'stitch-downscale = zetastitcher.scripts.stitch_downscale:main',
         ],

diff --git a/tests/test_filematrix.py b/tests/test_filematrix.py
@@ -4,7 +4,7 @@
 
 from ddt import ddt, data
 
-from zetastitcher.io.filematrix import parse_file_name
+from zetastitcher.align.filematrix import parse_file_name
 
 
 test_vectors = [

diff --git a/zetastitcher/__init__.py b/zetastitcher/__init__.py
@@ -1,5 +1,5 @@
 from .version import __version__
 
 from .io.inputfile import InputFile
-from .io.filematrix import FileMatrix
+from zetastitcher.align.filematrix import FileMatrix
 from .io.virtual_fused_volume import VirtualFusedVolume
diff --git a/zetastitcher/align/__init__.py b/zetastitcher/align/__init__.py
diff --git a/zetastitcher/runner.py → zetastitcher/align/__main__.py b/zetastitcher/runner.py → zetastitcher/align/__main__.py
@@ -16,14 +16,14 @@
 import numpy as np
 import pandas as pd
 
-from .io.inputfile import InputFile
-from .io.filematrix import FileMatrix
-from zetastitcher.io.xcorr_filematrix import XcorrFileMatrix
+from zetastitcher.io.inputfile import InputFile
+from zetastitcher.align.filematrix import FileMatrix
+from zetastitcher.align.xcorr_filematrix import XcorrFileMatrix
 from zetastitcher.fuse import absolute_positions
 from zetastitcher.fuse.__main__ import ABS_MODE_MAXIMUM_SCORE
 from .normxcorr import normxcorr2_cv
 
-from .version import __version__
+from zetastitcher.version import __version__
 
 
 logger = logging.getLogger(__name__)

diff --git a/zetastitcher/io/filematrix.py → zetastitcher/align/filematrix.py b/zetastitcher/io/filematrix.py → zetastitcher/align/filematrix.py
@@ -11,7 +11,7 @@
 import pandas as pd
 import networkx as nx
 
-from .inputfile import InputFile
+from zetastitcher.io.inputfile import InputFile
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())

diff --git a/zetastitcher/normxcorr.py → zetastitcher/align/normxcorr.py b/zetastitcher/normxcorr.py → zetastitcher/align/normxcorr.py
diff --git a/zetastitcher/io/xcorr_filematrix.py → zetastitcher/align/xcorr_filematrix.py b/zetastitcher/io/xcorr_filematrix.py → zetastitcher/align/xcorr_filematrix.py
diff --git a/zetastitcher/fuse/__main__.py b/zetastitcher/fuse/__main__.py
@@ -13,8 +13,8 @@
 
 from . import absolute_positions
 from .fuse_runner import FuseRunner
-from ..io.filematrix import FileMatrix
-from zetastitcher.io.xcorr_filematrix import XcorrFileMatrix
+from zetastitcher.align.filematrix import FileMatrix
+from zetastitcher.align.xcorr_filematrix import XcorrFileMatrix
 
 logger = logging.getLogger(__name__)
 coloredlogs.install(level='INFO', fmt='%(levelname)s [%(name)s]: %(message)s')

diff --git a/zetastitcher/io/virtual_fused_volume.py b/zetastitcher/io/virtual_fused_volume.py
@@ -10,7 +10,7 @@
 
 import numpy as np
 
-from .filematrix import FileMatrix
+from zetastitcher.align.filematrix import FileMatrix
 from .inputfile import InputFile
 from ..fuse.overlaps import Overlaps
 from ..fuse.fuse import fuse_queue

diff --git a/zetastitcher/scripts/stitch_downscale.py b/zetastitcher/scripts/stitch_downscale.py
@@ -8,7 +8,7 @@
 import numpy as np
 
 from zetastitcher import VirtualFusedVolume, FileMatrix
-from zetastitcher.io.xcorr_filematrix import XcorrFileMatrix
+from zetastitcher.align.xcorr_filematrix import XcorrFileMatrix
 
 
 logger = logging.getLogger(__name__)