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README example does not run; opens in read-only by default #52

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talonchandler opened this issue Feb 15, 2023 · 3 comments · Fixed by #54
Closed

README example does not run; opens in read-only by default #52

talonchandler opened this issue Feb 15, 2023 · 3 comments · Fixed by #54
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@ziw-liu
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bug Something isn't working documentation Improvements or additions to documentation
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0.1.0

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@talonchandler
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In the iohub's README we have:

with open_ome_zarr("20200812-CardiomyocyteDifferentiation14-Cycle1.zarr") as dataset:
    ...
    new_fov = dataset.create_position("A", "1", "0")  # creates a new fov
    ...

which fails because by default open_ome_zarr opens in read-only mode.

Adding mode='r+' works, but it modified/added to the dataset I downloaded from the web, then failed on subsequent runs (since the position already existed when I ran it the first time).

Maybe a more user-friendly README example should read the example dataset, write to a new file, then read+append to that new file?
@talonchandler
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PS I love .print_tree and the create_position API. Both are big steps forward compared to our old readers.

@ziw-liu
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ziw-liu commented Feb 15, 2023

Ah, I mistakenly deleted the file mode option mode="a" at some point. Will fix shortly.

@ziw-liu ziw-liu self-assigned this Feb 15, 2023
@ziw-liu ziw-liu added bug Something isn't working documentation Improvements or additions to documentation labels Feb 15, 2023
@ziw-liu
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ziw-liu commented Feb 15, 2023

Maybe a more user-friendly README example should read the example dataset, write to a new file, then read+append to that new file?

Great idea!

@ziw-liu ziw-liu mentioned this issue Feb 15, 2023
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@mattersoflight mattersoflight added this to the 0.1.0 milestone Feb 15, 2023
ziw-liu added a commit that referenced this issue Mar 14, 2023
@ziw-liu @camFoltz
@mattersoflight @talonchandler @ieivanov
Micro-Manager TIFF formats Converter (#76)
0bfb0e5 
* Merge pull request #14 from mehta-lab/QLIPP_pipeline

recOrder pipeline infrastructure + qlipp pipeline submodule

* Merge pull request #22 from mehta-lab/zarr_converter

Zarr converter

* Merge pull request #52 from mehta-lab/fluor_deconv

Fluorescence Deconvolution and PhaseFromBF pipelines

* Merge pull request #31 from mehta-lab/calibration_plugin

Calibration/Acquisition Plugin

* Merge pull request #112 from mehta-lab/cleanup-tests-and-readme

Improved testing, configs, and dev tools

* Merge pull request #123 from mehta-lab/zarr-converter-position-bug

Fix ome-tif to zarr converter for acquisitions with micromanager beta

* Merge pull request #140 from mehta-lab/restructure_tests

Restructure tests

* Merge pull request #148 from mehta-lab/pycromanager_converter_v2

Pycromanager converter v2

* Merge pull request #167 from mehta-lab/bkg-correction-fixes2

Fix background correction for non-square images and online mode

* Merge pull request #157 from mehta-lab/RAM-warning

Print RAM warning message in online and offline modes

* Merge pull request #169 from mehta-lab/warn-bkg-averaging

Remove background averaging

* Merge pull request #174 from mehta-lab/show-ram-warning

Show RAM warning in GUI / log in CLI

* Merge pull request #175 from mehta-lab/better-messages

Improved warning message

* Merge pull request #181 from mehta-lab/error-mismatched-bkg-and-img

Always load background and warn if background and image sizes are mismatched

* Merge pull request #182 from mehta-lab/error-mismatched-bkg-and-img

Mismatched x/y size of background and acquisition should error instead of warn

* Merge pull request #210 from mehta-lab/0.2.0-gui-hide

Remove fluorescence, preprocessing, and postprocessing; simplify GUI

* Merge pull request #219 from mehta-lab/0.2.0-integration

0.2.0 integration PR

* Introduce Black formatting into the code base (#229)

* black-format all `.py` files except recorder_ui.py

* create .git-blame-ignore-revs

* Document how to ignore formatting commits

* Document `git` version

Co-authored-by: Talon Chandler <talonchandler@gmail.com>

* draft refactor for imread

* expose primary entry points

* fix type check and tests

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* fix formatting

* update `imread` docstring

* define supported formats

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* rename pycromanager reader to ndtiff

Pycromanager is no longer a dependency, and MM can also write NDTIFF.

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* remove 'doesnt work' code

* improve error messages

* rearrange files from patch

* depend on tqdm for progress bar in conversion

* move util function

* delete other util functions

* make util function private

* remove redundant file

* rename converter file

* fix some of the references and docstrings

* draft refactor

* write with new ngff module

* fix position grid

* fix image check

* close writer after conversion

* test ome-tiff conversion

* handle invalid stage position metadata

* support labelling positions

* fix typo

* fix path type

* convert single page tiff datasets

This is rather broken: the reader does not handle metadata well

* allow longer conversion time in tests

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* draft cli command

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* fix argument

* detect flat ndtiff

* sort imports

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

* limit bar length

* add -h shortcut for help

* test cli

* fix get_image

* test against a random choice of dataset

---------

Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Co-authored-by: Cameron Foltz <56048121+camFoltz@users.noreply.github.com>
Co-authored-by: Shalin Mehta <shalin.mehta@gmail.com>
Co-authored-by: Talon Chandler <talonchandler@gmail.com>
Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org>
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Fix example in README czbiohub-sf/iohub
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