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Histogram refactor #58

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merged 6 commits into from
Apr 26, 2023
Merged

Histogram refactor #58

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fb9ceb2
Adding basic test for histgram for zarr files
blowekamp Apr 14, 2023
21993d8
Move build_histogram to utils
blowekamp Apr 14, 2023
1aad32b
Add visual_min_max procedure
blowekamp Apr 14, 2023
231eebb
Add logger to root of pytools package
blowekamp Apr 17, 2023
80eb517
Add debug info of dask configuration
blowekamp Apr 18, 2023
d96a426
Allow path to be string or Path object
blowekamp Apr 18, 2023
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10 changes: 7 additions & 3 deletions docs/api.rst
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Original file line number Diff line number Diff line change
@@ -1,19 +1,23 @@
API
===


.. automodule:: pytools
:members:

.. automodule:: pytools.meta
:members:

.. automodule:: pytools.utils.zarr
:members:

.. automodule:: pytools.convert
.. automodule:: pytools.utils.histogram
:members:

.. automodule:: pytools.ng.mrc2nifti
.. automodule:: pytools.convert
:members:

.. automodule:: pytools.ng.build_histogram
.. automodule:: pytools.ng.mrc2nifti
:members:

.. automodule:: pytools.zarr_rechunk
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9 changes: 2 additions & 7 deletions docs/commandline.rst
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Expand Up @@ -5,22 +5,17 @@ The Pytools packages contain a command line executables for various tasks. They

.. code-block :: bash
mrc_visual_min_max --help
mrc2nifti --help
Or the preferred way using the `python` executable to execute the module entry point:

.. code-block :: bash
python -m mrc_visual_min_max --help
python -m mrc2nifti --help
With either method of invoking the command line interface, the following sections describes the sub-commands available
and the command line options available.

.. click:: pytools.ng.mrc2nifti:main
:prog: mrc2nifti

.. click:: pytools.ng.mrc2ngpc:main
:prog: mrc2npgc

.. click:: pytools.ng.build_histogram:main
:prog: mrc_visual_min_max
1 change: 0 additions & 1 deletion pyproject.toml
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Expand Up @@ -42,7 +42,6 @@ local_scheme = "dirty-tag"

[project.scripts]
mrc2nifti = "pytools.ng.mrc2nifti:main"
mrc_visual_min_max = "pytools.ng.build_histogram:main"
zarr_rechunk = "pytools.zarr_rechunk:main"
zarr_build_multiscales = "pytools.zarr_build_multiscales:main"

11 changes: 10 additions & 1 deletion pytools/__init__.py
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Expand Up @@ -12,10 +12,19 @@
# limitations under the License.
#

from .workflow_functions import visual_min_max

import logging

logger = logging.getLogger(__name__)
del logging

_installed_package = "tomojs_pytools"

try:
from ._version import version as __version__
except ImportError:
pass

__all__ = ["__version__"]

__all__ = ["__version__", "visual_min_max", "logger"]
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