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| name: Generate README | ||
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| on: | ||
| pull_request: | ||
| paths: | ||
| - "docs/**/*" | ||
| workflow_run: | ||
| workflows: | ||
| - "generate_help_docs" | ||
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| jobs: | ||
| make-README: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: write | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Fill template | ||
| working-directory: "docs/" | ||
| timeout-minutes: 0.1 | ||
| run: | | ||
| sub_doc_parts_from() { | ||
| template="$1" | ||
| directory="$2" | ||
| for file in "$directory"/*; do | ||
| if [ -f "$file" ]; then | ||
| placeholder="{{ $(echo "${file^^}" | tr ./ _) }}" | ||
| echo "Saving $file to $placeholder with expanded environment variables" >&2 | ||
| # Export file contents to text following a pattern in template.md, e.g.: | ||
| # section/test_file.md would replace "{{ SECTION_TEST_FILE_MD }}"" | ||
| template="${template//"$placeholder"/"$(<"$file")"}" | ||
| fi | ||
| done | ||
| echo "$template" | ||
| } | ||
| # Fills from docs/sections sections, then docs/help (note "working-directory") | ||
| sub_doc_parts_from "$(sub_doc_parts_from "$(<template.md)" "sections")" "help">../README.md | ||
| - name: Setup git | ||
| run: | | ||
| git config --local user.name "github-actions[bot]" | ||
| git config --local user.email "github-actions[bot]@users.noreply.github.com" | ||
| git remote set-url origin https://${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} | ||
| - name: Push changes (if any) | ||
| run: | | ||
| git pull | ||
| if git update-index --refresh && git diff-index --quiet HEAD --; then | ||
| git add README.md | ||
| git commit -m "Automated update of README.md from docs" | ||
| branch_name="${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" | ||
| git push origin HEAD:$branch_name | ||
| fi |
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| name: Generate README | ||
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| on: | ||
| pull_request: | ||
| paths: | ||
| - "src/sim_recon/cli/parsing/*" | ||
| - "src/sim_recon/settings/formatting.py" | ||
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| jobs: | ||
| generate-help-docs: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| - name: Display Python version | ||
| run: python -c "import sys; print(sys.version)" | ||
| - name: Copy template | ||
| run: cp -f docs/template.md README.md | ||
| - name: Install (without dependencies) | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| python -m pip install . --no-deps | ||
| - name: Ensure README exists | ||
| run: | | ||
| if [ ! -f "README.md" ]; then | ||
| touch README.md | ||
| fi | ||
| - name: Get help strings from package | ||
| run: | | ||
| python -m sim_recon.cli.parsing.otf '--help' >docs/help/sim_otf.txt | ||
| python -m sim_recon.cli.parsing.recon '--help' >docs/help/sim_recon.txt | ||
| python -m sim_recon.cli.parsing.otf_view '--help' >docs/help/otf_view.txt | ||
| - name: Setup git | ||
| run: | | ||
| git config --local user.name "github-actions[bot]" | ||
| git config --local user.email "github-actions[bot]@users.noreply.github.com" | ||
| git remote set-url origin https://${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} | ||
| - name: Push changes (if any) | ||
| run: | | ||
| if git update-index --refresh && git diff-index --quiet HEAD --; then | ||
| git add docs/help/* | ||
| git commit -m "Automated update of help docs" | ||
| branch_name="${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" | ||
| git push origin HEAD:$branch_name | ||
| fi |
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| usage: otf-view [-h] [--show] [--show-only] [-o OUTPUT_DIRECTORY] [-v] | ||
| [--no-progress] | ||
| otf_paths [otf_paths ...] | ||
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| Create OTF views | ||
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| positional arguments: | ||
| otf_paths OTF file paths | ||
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| options: | ||
| -h, --help show this help message and exit | ||
| --show Display the plots while running | ||
| --show-only Show plots without saving | ||
| -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY | ||
| Save to this directory if saving plots, otherwise each | ||
| plot will be saved with its input file | ||
| -v, --verbose Show more logging | ||
| --no-progress turn off progress bars (only has an effect if tqdm is | ||
| installed) | ||
| sdfsdf |
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| usage: sim-otf [-c CONFIG_PATH] [-p PSF_PATHS [PSF_PATHS ...]] | ||
| [-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup] | ||
| [--shape XY_SHAPE XY_SHAPE] [-v] [--no-progress] | ||
| [--nphases NPHASES] [--ls LS] [--na NA] [--nimm NIMM] | ||
| [--background BACKGROUND] [--beaddiam BEADDIAM] [--angle ANGLE] | ||
| [--nocompen NOCOMPEN] [--fixorigin FIXORIGIN FIXORIGIN] | ||
| [--leavekz LEAVEKZ LEAVEKZ LEAVEKZ] [-h] | ||
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| SIM PSFs to OTFs | ||
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| options: | ||
| -c CONFIG_PATH, --config-path CONFIG_PATH | ||
| Path to the root config that specifies the paths to | ||
| the OTFs and the other configs | ||
| -p PSF_PATHS [PSF_PATHS ...], --psf PSF_PATHS [PSF_PATHS ...] | ||
| Paths to PSF files to be reconstructed (multiple paths | ||
| can be given) | ||
| -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY | ||
| If specified, the output directory that the OTFs will | ||
| be saved in, otherwise each OTF will be saved in the | ||
| same directory as its PSF | ||
| --overwrite If specified, files will be overwritten if they | ||
| already exist (unique filenames will be used | ||
| otherwise) | ||
| --no-cleanup If specified, files created during the OTF creation | ||
| process will not be cleaned up | ||
| --shape XY_SHAPE XY_SHAPE | ||
| Takes 2 integers (X Y), specifying the shape to crop | ||
| PSFs to before converting (powers of 2 are fastest) | ||
| -v, --verbose Show more logging | ||
| --no-progress turn off progress bars (only has an effect if tqdm is | ||
| installed) | ||
| -h, --help show this help message and exit | ||
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| Overrides: | ||
| Arguments that override configured values. Defaults stated are only used | ||
| if no value is given or configured. | ||
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| --nphases NPHASES Number of pattern phases per SIM direction | ||
| --ls LS Line spacing of SIM pattern in microns | ||
| --na NA Detection objective's numerical aperture | ||
| --nimm NIMM Refractive index of immersion medium | ||
| --background BACKGROUND | ||
| Camera readout background | ||
| --beaddiam BEADDIAM The diameter of the bead in microns, by default 0.12 | ||
| --angle ANGLE The k0 vector angle with which the PSF is taken, by | ||
| default 0 | ||
| --nocompen NOCOMPEN Do not perform bead size compensation, default False | ||
| (do perform) | ||
| --fixorigin FIXORIGIN FIXORIGIN | ||
| The starting and end pixel for interpolation along kr | ||
| axis, by default (2, 9) | ||
| --leavekz LEAVEKZ LEAVEKZ LEAVEKZ | ||
| Pixels to be retained on kz axis, by default (0, 0, 0) | ||
| sad |
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| ### CLI | ||
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| ##### sim-otf | ||
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| ``` | ||
| {{ HELP_SIM_OTF_TXT }} | ||
| ``` | ||
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| ##### sim-recon | ||
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| ``` | ||
| {{ HELP_SIM_RECON_TXT }} | ||
| ``` | ||
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| ##### otf-view | ||
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| ``` | ||
| {{ HELP_OTF_VIEW_TXT }} | ||
| ``` | ||
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| ##### dv2tiff | ||
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| Accepts a list of DV files to be converted to TIFFs (with some OME metadata). |
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| ### Configuration | ||
| Calls to `sim-otf` and `sim-recon` can both take a `-c`/`--config` argument. This should be similar to the `config.ini` file in the configs directory, which specifies the defaults config, any per-channel configs (some values should be set on a per-channel basis), and the locations of OTFs for each channel. | ||
| The channels are specified based on the emission wavelength in nanometres (must be an integer). | ||
| ##### Example: | ||
| For a channel with an emission wavelength of 525nm: | ||
| - In the `[configs]` section, the channel config can be specified as `525=/path/to/configs/525.cfg` | ||
| - In the `[otfs]` section, the channel OTF file can be specified as `525=/path/to/otfs/525_otf.tiff` | ||
| A directory can be specified within each of the `[configs]` and `[otfs]` sections. If given, files can also be defined relative to that directory, e.g. if `directory=/path/to`, then `525=/path/to/otfs/525_otf.tiff` could simply be `525=otfs/525_otf.tiff`. | ||
| Config settings will be overriden by higher-priority sources. | ||
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| ##### Order of setting priority: | ||
| 1. Command line arguments (override all) | ||
| 2. Per-channel configs (override defaults for the appropriate channel only) | ||
| 3. Defaults (override any cudasirecon defaults) |
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| # PySIMRecon | ||
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| Easy to use wrapper for pyCUDAsirecon, allowing the use of DV (DeltaVision) files without IVE/Priism (UCSF library with MRC/DV support). | ||
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| This is built for easy use from the command line or as part of an auto-processing pipeline, allowing parameters to be pre-configured or defined at runtime. | ||
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| ### Goal | ||
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| To reconstruct the SIM data and create OTFs from PSFs from the cryoSIM at B24, Diamond from the .dv files created by Cockpit. Requirements are: | ||
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| - Easy to use | ||
| - Open source | ||
| - Reproducable results | ||
| - Can be used as part of an automatic processing pipeline | ||
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| ### Current state | ||
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| Under development | ||
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| {{ SECTIONCONFIGURATION_MD }} | ||
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| {{ SECTIONS_COMMAND_LINE_MD }} |