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xystitch

This code is useful, but old and crusty. Don't look under the hood :)

Core utilities in typical usage order:

  • xy-stitch: high level .pto creation workflow (xy-feature + xy-pto)
    • xy-feature: create features
    • xy-pto: tweak pto and optimize it
  • xy-hugin: open reduced .pto for faster cropping and rotation
    • Or just use hugin if your project is small enough
  • xy-ts: stitch image into output .jpgs such as tiles and/or one large .jpg

Misc utilities:

  • xy-cphugin: open reduced .pto to tweak control points around poorly optimized areas
  • xy-outlier: print and remove control point outliers
  • xy-cp: similar to outlier, but operates on image RMS
  • xy-stack: stack image sets using Zerene Stacker. Used for distorted chips
  • xy-stitch-aj uses older algorithm that gave early good results

Quick start

Requires Python 3.6 or later

Tested on:

  • Ubuntu 20.04
  • python 3.8.5

Install:

# Misc requirements
sudo apt install hugin-tools enblend imagemagick python3-psutil
sudo pip3 install Pillow

# Do one of these:
# Option 1: install from pip
sudo pip3 install xystitch
# Option 2: install from git
cd ~
git clone https://github.com/JohnDMcMaster/xystitch.git
cd xystitch
sudo python3 setup.py install

Now try a small stitch:

wget https://siliconpr0n.org/media/xystitch/2020-11-27_stitch_test.tar
tar -xf 2020-11-27_stitch_test.tar
cd 2020-11-27_stitch_test
# Perform feature recognition and place images on a global position grid
# On my carbon X1 (gen 4) this took ~10 sec
xy-stitch

Now open in Hugin to rotate and crop the image (optional):

xy-hugin out.pto

If you want a quick result from Hugin:

  1. Click on interface => Simple
  2. Go to crop tab and set crop
  3. Save project (ctrl-S or file => save)
  4. Close the Hugin window

If you want a higher quality result from Hugin:

  1. Click on interface => Expert
  2. If you don't see a "Crop" tab already: Click on View menu => "Fast Panorama Preview Window"
  3. Go to projection tab. If image doesn't fit in the screen, increase field of view
  4. Go to move/drag tag and update Roll until image is level
  5. Go to crop tab and set crop
  6. Go back to the other Hugin window (might be called "Hugin - Panorrama Sticher")
  7. Go to stitcher tab and click "Calcualte Optimal Size"
  8. Save project (ctrl-S or file => save)
  9. Close both Hugin windows (closing the main window will close both)
# On my carbon X1 (gen 4) this took ~45 sec
xy-ts

If you'd like to see stitch progress, in a new window do "tail -f pr0nts/w00.log"

Output files:

  • single/: final .jpg, if its possible to make
  • st/: "supertiles,", the intermediate partial stitches
  • out/: tiles. Can be fed into pr0nmap utility
  • pr0nstitch/: log files

User guide

WARNING: there are several hard coded values in the framework right now. Please see "config" section to work around them until fixed.

Image file name

  • Name files like c012_r345.jpg to put an image at col=12, row=345
  • c000_r000.jpg is the first image
  • xy-feature can tolerate missing images by adding "--skip-missing"
  • There are several utlities to rename files into compliant form
    • Ex: rename_xy.py interpolates a manually taken image set with irregular columns into a grid layout

Stitch failures

  • Commands can fail if they out of memory
    • You will hopefully get a legible error message when this happens, even if nona/enblend is not by itself
    • Try reducing number of threads
    • Try reducing supertile size and/or use config file to increase their memory
    • Do you have enough disk space?
  • nona may fail if images have too much overlap and/or are cropped too close to effectively use an image
    • Consider making crop large
    • Try stitching with a different (usually larger is better) supertile size
    • xystitch tries hard to work around this but doesn't always succeed
    • I take images w/ about 30% overlap

Sample performance data: https://docs.google.com/spreadsheets/d/1zUHiHdVTUtuGzdpsjj1qhKfYHIgDBVzwJIBZmqQP_4c/edit?usp=sharing

Main config

Environment variables (see xystitch/config.py):

  • XY_STEP_FRAC_X, XY_STEP_FRAC_Y (or XY_STEP_FRAC): fraction of image that is stepped to move to next
    • Default: 0.70, but a scan specific config file, if present, will take preference over this variable
    • Ex: default of 0.70 means 30% overlap to adjacent image
      • If there is an image on each side 40% of the image (in the center) will be unique
    • This constant name / application needs review for clarity
  • XY_OVERLAP_OUTLIER_THRESH: throw out images that differ by more than given fraction vs expected overlap
    • Default: 0.10 (ie 10%) means that with default 0.70 overlap, a step size of 60% to 80% is acceptable

Main config file used for advanced operations like setting enblend max memory.

Suggestions for st_max_pix:

  • This is intended to stop jobs from taking too long more than prevent out of memory errors
  • Run a long job / without limit until you are getting tired of it completing
  • Ex: I aim that supertiles can stitch overnight, say complete within 8 hours
  • Consider using profile_enblend.py on a log file to plot how long images take to process
  • Convert to pixels...
  • Ex: 70% step size, 1632x1224 image: 0.7 * 1632 * 0.7 * 1224 = 0.98 MP / image. If 8 hours can process around 600 images, set limit to 0.98 * 600 = 588m
  • TODO: collect more data to conclusively show performance actually depends more on pixels than number images

Sample config file with commonly tweaked options:

$ cat ~/.xyrc
{
    "max_mem": "110g",
    "ts": {
        "st_max_pix": "600m"
    },
    "enblend": {
        "opts": "-m 6144"
    }
}

Sample config file with advanced configuration:

$ cat ~/.xyrc
{
    "max_mem": "110g",
    "temp_base": "/mnt/m10_4/tmp/",
    "keep_temp": 1,
    "ts": {
        "workers": 16,
        "st_max_pix": "600m"
    },
    "enblend": {
        "opts": "-m 6144"
    }
}

Importing sequentially named files

Files must be named to have upper left origin and 0 indexed rows/columns. rename_xy.py can be used to import files named sequentially, such as a DSLR might take

Munge order:

  • Apply column markers (--cols or --endrows)
  • Remove rows/columns (--rm-even-row etc)
  • Apply layout

Supported layouts:

  • lr-ud: images start at left and go right
  • rl-ud: iamges start at right and go left
  • serp-lr-ud: images start at top, go left and go right, then right and go left. Rinse and repeat
  • serp-rl-ud: images start at top, go right and go left, then left and go right. Rinse and repeat
  • serp-lr-du: like serp-lr-ud, but start from bottom instead of top
  • serp-rl-du: like serp-rl-ud, but start from bottom instead of top

Scan config

This file is output by pyuscope. It is used to automatically load scan parameters and shouldn't be required

TODO: add a link to config and/or describe options digested here

Ubuntu 20.04 notes

Had to adjust magick limits. Not carefully thought out but I'm using the values below

/etc/ImageMagick-6/policy.xml

<policy domain="resource" name="memory" value="16GiB"/>
<policy domain="resource" name="map" value="32GiB"/>
<policy domain="resource" name="width" value="128KP"/>
<policy domain="resource" name="height" value="128KP"/>
<!-- <policy domain="resource" name="list-length" value="128"/> -->
<policy domain="resource" name="area" value="16GB"/>
<policy domain="resource" name="disk" value="32GiB"/>

enblend eliminated -m option, which causes multiple issues with my stitches. TLDR: follow instructions below to setup enblend 4.1 and have something like below in your config

cat ~/.xyrc
{
    "enblend": {
        "opts": "-m 6144"
    }
}

Setup:

tar -xf enblend-enfuse-4.1.5.tar.gz
cd enblend-enfuse-4.1.5
sudo apt-get install -y libopenexr-dev libboost-system-dev \
  libboost-filesystem-dev libboost-graph-dev libboost-thread-dev \
  freeglut3-dev libglew-dev libxi-dev libxmu-dev libplot-dev libgsl0-dev \
  liblcms2-dev \
  \
  help2man texinfo gnuplot tidy \
  libvigraimpex-dev libgsl-dev libtiff5 libtiff5-dev
./configure  --prefix=/opt/enblend-4.1.5 --enable-gpu-support --enable-image-cache
time make -j $(nproc)
sudo make install
mkdir -p ~/bin
ln -s /opt/enblend-4.1.5/bin/enblend ~/bin/

Version history

v0.0.0 (2020-01-28)

  • Import old project from pr0ntools repository

v1.0.0 (2020-11-27)

  • First official release
  • Adopt xy- prefix

v1.1.0 (2021-03-06)

  • Python3
  • Fix optimizer RMS crash bug
  • Print worker status in master
  • Remove pr0ntools reference

v1.2.0 (future)

  • .pr0nrc => .xyrc
  • Change ts memory configuration
  • Clean up worker printing

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Microscope image stitching

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