abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Can not import 3D tiff stacks #101

Open tangmc0210 opened 1 day ago

tangmc0210 commented 1 day ago

I really appreciate your efforts for providing such an amazing tool for image stitch but I met some problems thatI am using a xml file to import my 3D tiff files but the terastitcher keeps crashing whether I use the GUI or the command line. I really need some help!

My command line is:

terastitcher --import --projin=F:/terastc_test/xml_import.xml --volin_plugin=tiff3D

My file tree is shown below and each .tif file is an 3d tiff file with the shape (100, 2048, 2048) as (z, x, y).

(base) PS F:\terastc_test> tree /f
Folder PATH listing for volume Data
Volume serial number is F49A-B84B
F:.
│   xml_import.xml
│
├───TestTile001
│       000001.tif
│
├───TestTile002
│       000002.tif
│
├───TestTile003
│       000003.tif
│
└───TestTile004
        000004.tif

My import xml file is like this:

<TeraStitcher volume_format="TiledXY|3Dseries" input_plugin="tiff3D">
<stacks_dir value="F:/terastc_test"/>
<ref_sys ref1="1" ref2="2" ref3="3"/>
<voxel_dims V="2.0" H="2.0" D="1.0"/>
<origin V="0" H="0" D="0"/>
<mechanical_displacements V="1000" H="1000"/>
<dimensions stack_rows="2" stack_columns="2" stack_slices="100"/>
<STACKS>
<Stack N_BLOCKS="1" BLOCK_SIZES="100" BLOCKS_ABS_D="0" N_CHANS="1" N_BYTESxCHAN="1" ROW="1" COL="1" ABS_V="2048" ABS_H="2048" ABS_D="0" STITCHABLE="no" DIR_NAME="TestTile001" Z_RANGES="[0,100)" IMG_REGEX="">
<NORTH_displacements/>
<EAST_displacements/>
<SOUTH_displacements/>
<WEST_displacements/>
</Stack>
<Stack N_BLOCKS="1" BLOCK_SIZES="100" BLOCKS_ABS_D="0" N_CHANS="1" N_BYTESxCHAN="1" ROW="1" COL="0" ABS_V="2048" ABS_H="" ABS_D="0" STITCHABLE="no" DIR_NAME="TestTile002" Z_RANGES="[0,100)" IMG_REGEX="">
<NORTH_displacements/>
<EAST_displacements/>
<SOUTH_displacements/>
<WEST_displacements/>
</Stack>
<Stack N_BLOCKS="1" BLOCK_SIZES="100" BLOCKS_ABS_D="0" N_CHANS="1" N_BYTESxCHAN="1" ROW="0" COL="1" ABS_V="" ABS_H="2048" ABS_D="0" STITCHABLE="no" DIR_NAME="TestTile003" Z_RANGES="[0,100)" IMG_REGEX="">
<NORTH_displacements/>
<EAST_displacements/>
<SOUTH_displacements/>
<WEST_displacements/>
</Stack>
<Stack N_BLOCKS="1" BLOCK_SIZES="100" BLOCKS_ABS_D="0" N_CHANS="1" N_BYTESxCHAN="1" ROW="0" COL="0" ABS_V="" ABS_H="" ABS_D="0" STITCHABLE="no" DIR_NAME="TestTile004" Z_RANGES="[0,100)" IMG_REGEX="">
<NORTH_displacements/>
<EAST_displacements/>
<SOUTH_displacements/>
<WEST_displacements/>
</Stack>
</STACKS>
</TeraStitcher>
tangmc0210 commented 1 day ago

As supplements, the tiff are np.uint16 and I am running the code on windows10 64bit. My computer is equipped with 128GB memory and a NVIDIA RTX 3090.

tangmc0210 commented 1 day ago

Supplements again, I am using the GUI version TeraStitcher-Qt5-1.10.18 and command line version TeraStitcher-portable-1.11.10-win64. Downloaded from Binary-packages.