deploy: 017c434

Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: aad7ffbc9e324db917903ba8efaf39c0
+tags: 645f666f9bcd5a90fca523b33c5a78b7

build/html/_sources/index.rst.txt

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+.. microDL documentation master file, created by
+   sphinx-quickstart on Tue Dec 13 10:33:59 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to microDL's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Introduction:
+
+microDL is a deep learning framework for processing microscopy data.
+The framework consists of:
+
+* Preprocessing: Flatfield correction, mask creation and normalization.
+* Training: Building and training 2.5D or 2D U-Net models for regression or segmentation.
+* Inference: Use your trained model to predict full size images.
+
+These pages offers in depth descriptions of the functions and classes of microDL and is mainly
+intended for developers,
+and users who would like to understand the details.
+If you're a user and are mainly interested in understanding how to run microDL,
+please see the `GitHub repository <https://github.com/mehta-lab/microDL>`_ and the readme markdown files within it.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

build/html/_sources/micro_dl.cli.rst.txt

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+micro\_dl.cli module
+=====================
+
+Submodules
+----------
+
+micro\_dl.cli.dataset\_pooling module
+-------------------------------------
+
+.. automodule:: micro_dl.cli.dataset_pooling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.cli.inference\_script module
+--------------------------------------
+
+.. automodule:: micro_dl.cli.inference_script
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.cli.metrics\_script module
+------------------------------------
+
+.. automodule:: micro_dl.cli.metrics_script
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.cli.preprocess\_script module
+---------------------------------------
+
+.. automodule:: micro_dl.cli.preprocess_script
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.cli.train\_script module
+----------------------------------
+
+.. automodule:: micro_dl.cli.train_script
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:

build/html/_sources/micro_dl.inference.rst.txt

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+micro\_dl.inference module
+===========================
+
+Submodules
+----------
+
+micro\_dl.inference.evaluation\_metrics module
+----------------------------------------------
+
+.. automodule:: micro_dl.inference.evaluation_metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.inference.image\_inference module
+-------------------------------------------
+
+.. automodule:: micro_dl.inference.image_inference
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.inference.model\_inference module
+-------------------------------------------
+
+.. automodule:: micro_dl.inference.model_inference
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.inference.stitch\_predictions module
+----------------------------------------------
+
+.. automodule:: micro_dl.inference.stitch_predictions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.inference
+   :members:
+   :undoc-members:
+   :show-inheritance:

build/html/_sources/micro_dl.input.rst.txt

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+micro\_dl.input module
+=======================
+
+Submodules
+----------
+
+micro\_dl.input.dataset module
+------------------------------
+
+.. automodule:: micro_dl.input.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.input.dataset\_with\_mask module
+------------------------------------------
+
+.. automodule:: micro_dl.input.dataset_with_mask
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.input.inference\_dataset module
+-----------------------------------------
+
+.. automodule:: micro_dl.input.inference_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.input.training\_table module
+--------------------------------------
+
+.. automodule:: micro_dl.input.training_table
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.input
+   :members:
+   :undoc-members:
+   :show-inheritance:

build/html/_sources/micro_dl.networks.layers.rst.txt

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+micro\_dl.networks.layers module
+=================================
+
+Submodules
+----------
+
+micro\_dl.networks.layers.interp\_upsampling2D module
+-----------------------------------------------------
+
+.. automodule:: micro_dl.networks.layers.interp_upsampling2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.layers.interp\_upsampling3D module
+-----------------------------------------------------
+
+.. automodule:: micro_dl.networks.layers.interp_upsampling3D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.networks.layers
+   :members:
+   :undoc-members:
+   :show-inheritance:

build/html/_sources/micro_dl.networks.rst.txt

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+micro\_dl.networks module
+==========================
+
+Submodules
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   micro_dl.networks.layers
+
+Submodules
+----------
+
+micro\_dl.networks.base\_conv\_net module
+-----------------------------------------
+
+.. automodule:: micro_dl.networks.base_conv_net
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.base\_image\_to\_vector\_net module
+------------------------------------------------------
+
+.. automodule:: micro_dl.networks.base_image_to_vector_net
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.base\_unet module
+------------------------------------
+
+.. automodule:: micro_dl.networks.base_unet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.conv\_blocks module
+--------------------------------------
+
+.. automodule:: micro_dl.networks.conv_blocks
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.image2D\_to\_vector\_net module
+--------------------------------------------------
+
+.. automodule:: micro_dl.networks.image2D_to_vector_net
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.image3D\_to\_vector\_net module
+--------------------------------------------------
+
+.. automodule:: micro_dl.networks.image3D_to_vector_net
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.unet2D module
+--------------------------------
+
+.. automodule:: micro_dl.networks.unet2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.unet3D module
+--------------------------------
+
+.. automodule:: micro_dl.networks.unet3D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.unet\_stack\_2D module
+-----------------------------------------
+
+.. automodule:: micro_dl.networks.unet_stack_2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.unet\_stack\_stack module
+--------------------------------------------
+
+.. automodule:: micro_dl.networks.unet_stack_stack
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+micro\_dl.networks.vqnet module
+-------------------------------
+
+.. automodule:: micro_dl.networks.vqnet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.networks
+   :members:
+   :undoc-members:
+   :show-inheritance:

build/html/_sources/micro_dl.plotting.rst.txt

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+micro\_dl.plotting module
+==========================
+
+Submodules
+----------
+
+micro\_dl.plotting.plot\_utils module
+-------------------------------------
+
+.. automodule:: micro_dl.plotting.plot_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: micro_dl.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance: