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Coordinate systems and new coordinate transformations proposal #138

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Coordinate systems and new coordinate transformations proposal #138

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Commits on Feb 1, 2022

  1. start of named space and transform metadata

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Commits on Feb 9, 2022

  1. fwd and inv coordinate transforms

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  2. Merge remote-tracking branch 'upstream/main' into coord-transforms 

    # Conflicts:
#	latest/index.bs
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  3. more transform details 

    * define pixel center coordinate system
* add input/output_axes
* add transform inverse flag
* add affine transform type
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  4. start page on details and recommendations

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Commits on May 5, 2022

  1. transformation progress 

    * flesh out array space
* define array indexing
* add more transformation types
* start transformation details section and examples
* update example
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Commits on May 9, 2022

  1. change fields to camelCase

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Commits on May 12, 2022

  1. add details for coordinate and displacement fields

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Commits on May 13, 2022

  1. add details on dimension order

    @bogovicj
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  2. clean up array indexing section

    @bogovicj
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Commits on May 15, 2022

  1. add more details for scale, translation, displacement

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Commits on May 16, 2022

  1. merge and cleanup

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Commits on May 24, 2022

  1. Merge remote-tracking branch 'upstream/main' into coord-transforms 

    # Conflicts:
#	latest/index.bs
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Commits on Jun 1, 2022

  1. clarify input and output dimensionality for transforms 

    * use "input" and "output" rather than '*Space' and '*Axes'
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Commits on Jun 3, 2022

  1. update to transformations 

    * reorder details
* clean up table
* add rotation
* details for sequence
* describe inverses
* wrap examples
    @bogovicj
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  2. rotation transformation details 

    * rephrase matrix storage
    bogovicj committed Jun 3, 2022
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  3. minor rephrase intro to coordinateTransformations section

    bogovicj committed Jun 3, 2022
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Commits on Jun 6, 2022

  1. add details for bijection ct 

    * change to "coordinates", removing "Field"
* change to "displacements", removing "Field"
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Commits on Jun 9, 2022

  1. big changes to transformations spec 

    * add details for transformation types
* (identity, inverseOf, bijection)
* describe inputAxes and outputAxes
* add new examples
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Commits on Sep 6, 2022

  1. Add "coordinateSystems" and "coordinateTransformations" fields for ex… 

    …amples

* some clean up
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Commits on Sep 7, 2022

  1. coordinate transformation updates: 

    * add mapIndex, mapAXis
* add examples
* affine stored as flat array only
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Commits on Sep 11, 2022

  1. update multiscales_example

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  2. rename dimensionWise byDimension 

    * sequence does not have by-dimension behavior
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  3. add more transformation examples

    @bogovicj
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  4. byDimension examples, rm input/outputAxes fields

    @bogovicj
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Commits on Sep 15, 2022

  1. reorder, simplify sections. 

    * flesh out some examples
    bogovicj committed Sep 15, 2022
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  2. clean up example formatting

    bogovicj committed Sep 15, 2022
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Commits on Sep 16, 2022

  1. add array coordinate system example

    bogovicj committed Sep 16, 2022
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Commits on Sep 23, 2022

  1. rm duplicate editor names, typo fix

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  2. fix sequence example json. add inverseOf to input/output field exception

    bogovicj committed Sep 23, 2022
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  3. be clearer re: half-open interval

    bogovicj committed Sep 23, 2022
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Commits on Oct 4, 2022

  1. move axes section into coordinateSystems section

    @bogovicj
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  2. typo fixes

    @bogovicj
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  3. Merge branch 'coord-transforms' of github.com:bogovicj/ngff into coor… 

    …d-transforms

# Conflicts:
#	latest/index.bs
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  4. add two new coordinate transformation examples 

    * multiscales dataset-level
* xarray like coordinates / byDimension
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  5. Allow tests to access all schemas

    @ivirshup
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  6. Fix how schemas are matched to examples

    @ivirshup
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  7. Add initial coordinate system schemas

    @ivirshup
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  8. Add array coordinate schema

    @ivirshup
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  9. Add test for array coordinate system

    @ivirshup
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  10. Stop adding cases for .config files

    @ivirshup
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Commits on Oct 5, 2022

  1. describe where to store coordinateTransformations

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  2. corrections for coordinates and displacements

    @bogovicj
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Commits on Oct 6, 2022

  1. add optional "longName" field for axes 

    see ome#142
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Commits on Oct 9, 2022

  1. Merge branch 'coord-transforms' into coord-transforms-schemas

    @ivirshup
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  2. Add longName property to axes schema

    @ivirshup
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  3. Add mapAxis and mapIndex schemas

    @ivirshup
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  4. Add affine transfrom, use reference for path_w_url

    @ivirshup
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  5. Move rotation example to example directory

    @ivirshup
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  6. Add schema for rotation

    @ivirshup
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  7. Move inverseOf example to examples directory

    @ivirshup
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  8. Added schema for inverseOf 

    Note that the test currently does not pass because displacements have not been defined yet.
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  9. Added byDimension transformation 

    The tests mark invalid pass because we would need dynamic validation to check whether the axes were present in the coordinate spaces.
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  10. Sequence schemas

    @ivirshup
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Commits on Oct 12, 2022

  1. Merge remote-tracking branch 'upstream/main' into coord-transforms 

    # Conflicts:
#	latest/index.bs
    @bogovicj
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  2. Move rotation example to example directory

    @ivirshup @bogovicj
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  3. Merge branch 'coord-transforms' into coord-transforms-schemas 

    Now that main has been merged into coord-transforms
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  4. Move inverseOf example to examples directory

    @ivirshup @bogovicj
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  5. multiscales example relative typo fix

    @bogovicj
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  6. corrections and clarifications to coordinates and displacements 

    * move bijection examples to separate files
* add axis types to xarrayLike example
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  7. transforms MUST have "input"

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Commits on Mar 14, 2023

  1. cts: remove url parameters

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  2. ct: fix and clarify nested json representation for affine and rotatio… 

    …n types
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Commits on Mar 15, 2023

  1. motivate coordinate systems 

    * add an example
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  2. describe discrete axes, interpolation, etc

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Commits on Sep 19, 2023

  1. spec: remove 5D limits

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Commits on Oct 10, 2023

  1. tforms: more details to conforming readers

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  2. tforms: more sensible output name for sequence transform example

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  3. tforms: typo fix

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  4. tforms: fix name of zgroup in example hierarchy comment

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  5. Merge remote-tracking branch 'dvb/coord-transforms' into coord-transf… 

    …orms
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  6. fix header and link for axes metadata

    @bogovicj
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  7. example coordinate systems follow recommendations

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  8. rm mapIndex transformation 

    * prefer using mapAxis
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Commits on Oct 11, 2023

  1. start of coordinatTransformations schema

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Commits on Oct 12, 2023

  1. missing_scale and duplicate_scale are valid

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Commits on Nov 22, 2023

  1. Merge branch 'coord-transforms' into coord-transforms-schemas

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Commits on Dec 4, 2023

  1. rm mapIndex examples 

    * mapIndex no longer part of the spec
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  2. affine parameters can be nested arrays

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  3. rm mapIndex from transform schema

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  4. add bijection transformation to schema

    @bogovicj
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  5. add displacements and coordinates transformations to schema 

    * preliminary
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Commits on Dec 5, 2023

  1. update tests with coordinateSystems

    @bogovicj
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  2. update image schema with coordinate systems

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  3. axis schema: don't enforce types

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  4. test: strict_image add coordinateSystems

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  5. test image, strict_image add input/output to transforms

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  6. start to modularize coordinate systems and transforms schemas 

    * reference in image schema
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Commits on Dec 6, 2023

  1. axes schema: allow at most three space axes

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  2. image_suite - one axis is valid

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  3. image_suite - two scales are valid, but not recommended

    @bogovicj
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  4. edit subspace example

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  5. coordinate_transformation arrays may not be empty

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  6. edit example byDimension2

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  7. edit multiscales examples

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  8. add schema config for subspace examples

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  9. rm coordinate_transforms.schema 

    * refactored into coordinate_transformation.schema and coordinate_systems_and_transforms.schema
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Commits on Dec 7, 2023

  1. multiscales-strict, re-order coordinate systems 

    * minor formatting
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  2. schema: add strict_axes, and strict_coordinate_systems 

    * update strict_image accordingly
* add an invalid strict_multiscales example (custom axis)
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Commits on Dec 8, 2023

  1. Merge remote-tracking branch 'origin/coord-transforms-schemas' into c… 

    …oord-transforms
    @bogovicj
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  2. correct byDimensionXarray transform example 

    * explicitly add array coordinate system
* add input field to transform
    @bogovicj
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  3. "units" -> "unit"

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Commits on Jul 25, 2024

  1. toward clarity on axis order 

    * changed example axis names to follow current convention
* TODO coordinate/displacement field vector order
* thanks @thewtex
    @bogovicj
    bogovicj committed Jul 25, 2024
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  2. typo fix

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    bogovicj committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. rm spurious / in <img> 

    * fixes rendering using new bikeshed
    @bogovicj
    bogovicj committed Jul 26, 2024
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Commits on Jul 27, 2024

  1. clarify axis order for coordinate and displacement fields 

    * including on-disk representation
* add an example
    @bogovicj
    bogovicj committed Jul 27, 2024
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  2. minor rephrasing in inverseOf

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    bogovicj committed Jul 27, 2024
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Commits on Jul 28, 2024

  1. toward resolving ambiguity in "sequence" transformations 

    * thanks @LucaMarconato
    @bogovicj
    bogovicj committed Jul 28, 2024
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Commits on Jul 29, 2024

  1. add anchors for transformation types

    @bogovicj
    bogovicj committed Jul 29, 2024
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  2. clarification on affine and rotation transformation 

    * adds section on matrix transformations
    @bogovicj
    bogovicj committed Jul 29, 2024
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  3. minor rephrasing 

    * prefer "shape" to "size" for zar arrays
    @bogovicj
    bogovicj committed Jul 29, 2024
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Commits on Aug 13, 2024

  1. remove reference to non-existent note

    @bogovicj
    bogovicj committed Aug 13, 2024
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  2. matrix transformations MUST be stored as 2D (json or zarr) arrays

    @bogovicj
    bogovicj committed Aug 13, 2024
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  3. typo affine -> rotation

    @bogovicj
    bogovicj committed Aug 13, 2024
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Commits on Aug 28, 2024

  1. merge edits from rfc 

    thanks @d-v-b
    @bogovicj
    bogovicj committed Aug 28, 2024
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  2. change examples to relative paths 

    thanks @normanrz
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    bogovicj committed Aug 28, 2024
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Commits on Sep 20, 2024

  1. typo and other minor fixes 

    thanks @LucaMarconato
    @bogovicj
    bogovicj committed Sep 20, 2024
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Commits on Sep 23, 2024

  1. fix affine matrix size, and other small fixes 

    thanks @LucaMarconato
    @bogovicj
    bogovicj committed Sep 23, 2024
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  2. correctly close code block

    @bogovicj
    bogovicj committed Sep 23, 2024
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  3. clarify invertibility of sequence transformation

    @bogovicj
    bogovicj committed Sep 23, 2024
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Commits on Sep 25, 2024

  1. fix byDimension header link

    @bogovicj
    bogovicj committed Sep 25, 2024
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  2. flesh out description for coordinates and displacements

    @bogovicj
    bogovicj committed Sep 25, 2024
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