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feat: Updates to the alignment entity #298
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return None | ||
@classmethod | ||
def get_name_and_path(cls, metadata: dict, name: str, path: str, results: dict[str, str]) -> [str, str, dict]: | ||
paths = {filname: filname for filname in metadata.get("files", [])} |
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typo: filename
vs filname
format: OPTIONAL ENUM (IMOD, ARETOMO) | ||
method_type: OPTIONAL ENUM (fiducial_based, patch_tracking, projection_matching) | ||
is_portal_standard: OPTIONAL, BOOLEAN (DEFAULT FALSE) | ||
offset: OPTIONAL |
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thanks for adding these
@@ -34,7 +36,7 @@ def upgrade_config(data: dict[str, Any]) -> dict[str, Any]: | |||
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def has_changes(file, config): | |||
with open(file, 'r') as file: |
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I think our formatters disagree
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wdym? 😅
@@ -817,7 +817,7 @@ classes: | |||
offset: | |||
description: *desc_alignment_offset | |||
range: AlignmentOffset | |||
volume_dimesion: | |||
volume_dimension: |
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good catch
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LGTM after the typo is fixed
* Updates to schema and template * Fixing tests * Adding files to alignments metadata * Update the alignment configs method type * Fixing typo * Adding undefined alignment_method_type
* Updating tomograms * updates to tomogram processing * updates to tomogram key photo filename * updates to tomogram neuroglance filepath * cleaning up tomogram and related entities * Updating tiltseries with identifiers * Updating alignment for tomogram relations * Adding alignment metadatapath to annotations and tomograms * Updating the paths * Updating the paths * Updating failed tests * Working tests clean up needed * fix: workaround for docker compose bugs. (#295) * fix: support filtering entities by related object id's (#296) * fix: support filtering entities by related object id's * chore: add seed script. (#297) * feat: Updates to the alignment entity (#298) * Updates to schema and template * Fixing tests * Adding files to alignments metadata * Update the alignment configs method type * Fixing typo * Adding undefined alignment_method_type * chore: Documenting the Jensen config generation (#293) * Adds comments to jensen config generation * Adding guardrails * Clean up * fix: method_name * chore: Update footer of release please PR's. (#299) * Adding tests * cleaning up the paths * Cleaning up paths * fix tests * Updating tomogram id generation * Updating viz_config generation * Making id directories * Making id directories * Making annotation id directory * Cleaning up paths with id * Updating neuroglancer precompute for dir structure * Updating neuroglancer config for dir structure * Updating raw tilt import to tiltseries_id directory * Fixing dependency on existing metadata * Adding documentation comment --------- Co-authored-by: Jessica Gadling <jgadling@chanzuckerberg.com>
* Updating tomograms * updates to tomogram processing * updates to tomogram key photo filename * updates to tomogram neuroglance filepath * cleaning up tomogram and related entities * Updating tiltseries with identifiers * Updating alignment for tomogram relations * Adding alignment metadatapath to annotations and tomograms * Updating the paths * Updating the paths * Updating failed tests * Working tests clean up needed * fix: workaround for docker compose bugs. (#295) * fix: support filtering entities by related object id's (#296) * fix: support filtering entities by related object id's * chore: add seed script. (#297) * feat: Updates to the alignment entity (#298) * Updates to schema and template * Fixing tests * Adding files to alignments metadata * Update the alignment configs method type * Fixing typo * Adding undefined alignment_method_type * chore: Documenting the Jensen config generation (#293) * Adds comments to jensen config generation * Adding guardrails * Clean up * fix: method_name * chore: Update footer of release please PR's. (#299) * Adding tests * cleaning up the paths * Cleaning up paths * fix tests * Updating tomogram id generation * Updating viz_config generation * Making id directories * Making id directories * Making annotation id directory * Cleaning up paths with id * Updating neuroglancer precompute for dir structure * Updating neuroglancer config for dir structure * Updating raw tilt import to tiltseries_id directory * Migration script * Update for tomograms * Adding support for alignments * Migrating annotation precompute * Migrating collection_metadata * Migrating rawtilt and gains * Clean up * Clean up * Clean up * Enabling the move * Adding metadata updates * Uncommenting deletion * Adding check before move * Adding wdl * minor fixes * Updating enqueue script * Updating annotation file names * Updating the tomogram key photo path * Fixing tests * Fix key_photo migration * Handling default alignments * fix path standardization when bucket name not in path * Lint. --------- Co-authored-by: Jessica Gadling <jgadling@chanzuckerberg.com>
Relates to
Description
Changes to the config schema:
is_canonical
->is_portal_standard
method_type
Changes to the configs:
alignment.method_type
in the config. It follows the following conditions:S3 Workflows:
get_name_and_path
class method to the AlignmentImporter. This allows the DestinationFilterFinder to reference an existing Alignment.