Update the manual for 4.0.0 (CellProfiler#4160)

* Add new modules, remove outdated one * Update objectprocessing.rst * Update CONTRIBUTING.md * add core, misc fixes * use new help file locations * indent * only image errors left * add CellProfiler3 paper * Remove outdated material * Remove outdated info * New texture stuff
glencoesoftware · Aug 22, 2020 · 07b9201 · 07b9201
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,6 +9,9 @@ This document provides guidelines for contributing to CellProfiler. You'll find
 
 We'd like to ensure this document is always accurate and understandable. Please [file an issue](https://github.com/CellProfiler/CellProfiler/issues/new) if any information is missing, unclear, or incorrect.  
 
+You may also check out our [YouTube tutorial](https://youtu.be/fgF_YueM1b8) for a discussion of many of these issues and demonstration of editing and creating 
+modules.
+
 ## Creating an Issue
 
 The CellProfiler team uses [GitHub issues](https://github.com/CellProfiler/CellProfiler/issues) to track upcoming and ongoing work. Examples of issues are:
@@ -146,6 +149,16 @@ In this section we provide a general outline of the process for submitting chang
   ```
 
   Your master branch now includes your change. Congratulations on a successful contribution!
+
+## Creating entirely new modules
+
+We love when our users create entirely new functionalities that have never existed in CellProfiler before! If you think your new module is useful to the 
+community, we invite you to contribute it as a plugin to the [CellProfiler-plugins](https://github.com/CellProfiler/CellProfiler-plugins) repository.  
+Contributed plugins may be moved into the main CellProfiler program (with author permission), depending on a number of factors including (but not limited to)
+1. Additional complexity and/or package dependencies added to the code
+1. Broad usefulness to the community
+1. Conflicts or overlap with other modules
+1. Our team's bandwidth to commit to maintaining your module in the future
 
 ## Style Guide
 

diff --git a/cellprofiler/data/help/legacy_matlab_image.rst b/cellprofiler/data/help/legacy_matlab_image.rst
@@ -7,11 +7,11 @@ illumination correction functions generated by **CorrectIlluminationCalculate**.
 These images could be loaded and applied to other pipelines using
 **CorrectIlluminationApply**.
 
-This version of CellProfiler no longer supports exporting MATLAB format
-images. Instead, the recommended image format for illumination correction
-functions is NumPy (.npy). Loading MATLAB format images is deprecated and
-will be removed in a future version of CellProfiler. To ensure compatibility
-with future versions of CellProfiler you can convert your .mat files to .npy
-files via **SaveImages** using this version of CellProfiler.
+This version of CellProfiler no longer supports reading or exporting 
+MATLAB format images. Instead, the recommended image format for illumination 
+correction functions is NumPy (.npy). Loading MATLAB format images can only be
+done in CellProfiler versions through 3.1.9. To ensure compatibility with future 
+versions of CellProfiler you can convert your .mat files to .npy
+files via **SaveImages** using any 3.X build of CellProfiler.
 
-See **SaveImages** for more details on saving NumPy format images.
+See **SaveImages** for more details on saving NumPy format images.
diff --git a/cellprofiler/data/help/other_batch.rst b/cellprofiler/data/help/other_batch.rst
@@ -68,10 +68,9 @@ cluster.
    processing large batches of images, you may also consider adding
    **ExportToDatabase** to your pipeline, after your measurement modules
    but before the CreateBatchFiles module. This module will export your
-   data either directly to a MySQL/SQLite database or into a set of
-   comma-separated files (CSV) along with a script to import your data
-   into a MySQL database. Please refer to the help for these modules in
-   order learn more about which settings are appropriate.
+   data either directly to a MySQL or SQLite database. Please refer to 
+   the help for these modules in order learn more about which settings 
+   are appropriate.
 #. *Run the pipeline to create a batch file.* Click the *Analyze images*
    button and the analysis will begin processing locally. Do not be
    surprised if this initial step takes a while: CellProfiler must
@@ -94,7 +93,7 @@ cluster.
    ::
 
       ./python -m cellprofiler -p <Default_Output_Folder_path>/Batch_data.h5 \\
-      -c -r -b \\
+      -c -r \\
       -f <first_image_set_number> \\
       -l <last_image_set_number>
 
@@ -109,8 +108,6 @@ cluster.
    -  ``-c``: Run “headless”, i.e., without the GUI
    -  ``-r``: Run the pipeline specified on startup, which is contained
       in the batch file.
-   -  ``-b``: Do not build extensions, since by this point, they should
-      already be built.
    -  ``-f <first_image_set_number>``: Start processing with the image
       set specified, <first\_image\_set\_number>
    -  ``-l <last_image_set_number>``: Finish processing with the image

diff --git a/cellprofiler/data/help/output_measurements.rst b/cellprofiler/data/help/output_measurements.rst
@@ -51,27 +51,31 @@ Below is the description for each of the terms:
    -  Measurements from *Intensity*, *Granularity*, *Children*,
       *RadialDistribution*, *Parent* and *AreaOccupied* categories will
       have an associated image as the Parameter.
-   -  *Measurements from the *Neighbors* and *Texture* category will
-      have a spatial scale ``Parameter``.*
+   -  Measurements from the *Neighbors* and *Texture* category will
+      have a spatial scale ``Parameter``.
    -  Measurements from the *Texture* and *RadialDistribution*
       categories will have both a spatial scale and an image
       ``Parameter``.
+   -  Measurements from the *Texture* category will have a spacial 
+      scale, image, and grayscale count ``Parameter``.
 
 As an example, consider a measurement specified as
-``Nuclei_Texture_DifferenceVariance_ER_3``:
+``Nuclei_Texture_DifferenceVariance_ER_3_256``:
 
 -  ``MeasurementType`` is “Nuclei,” the name given to the detected
    objects by the user.
 -  ``Category`` is “Texture,” indicating that the module
    **MeasureTexture** produced the measurements.
 -  ``SpecificFeatureName`` is “DifferenceVariance,” which is one of the
    many texture measurements made by the **MeasureTexture** module.
--  There are two ``Parameters``, the first of which is “ER”. “ER” is the
+-  There are three ``Parameters``, the first of which is “ER”. “ER” is the
    user-provided name of the image in which this texture measurement was
    made.
 -  The second ``Parameter`` is “3”, which is the spatial scale at which
    this texture measurement was made, according to the user-provided
    settings for the module.
+-  The final ``Parameter`` is "256", which is the number of gray levels
+   used in calculating the texture.
 
 See also the *Available measurements* heading under the main help for
 many of the modules, as well as **ExportToSpreadsheet** and

diff --git a/cellprofiler/data/help/pipelines_building.rst b/cellprofiler/data/help/pipelines_building.rst
@@ -111,8 +111,7 @@ panel* (located on the left-hand side of the CellProfiler window).
       time remaining to process the full image set.
 
    At the end of each cycle:
-
-   -  If you are creating a MATLAB or HDF5 output file, CellProfiler saves the measurements in the output file.
+
    -  If you are using the **ExportToDatabase** module, CellProfiler saves the measurements in the
       output database.
    -  If you are using the **ExportToSpreadsheet** module, CellProfiler saves the measurements *into a

diff --git a/cellprofiler/modules/closing.py b/cellprofiler/modules/closing.py
@@ -4,7 +4,7 @@
 
 **Closing** is the erosion of the dilation of an image. It’s used to
 remove pepper noise (small dark spots) and connect small bright cracks. 
-See `this tutorial`_ for more information.
+See `this tutorial <https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#closing>`__ for more information.
 
 |
 
@@ -14,8 +14,6 @@
 YES          YES           NO
 ============ ============ ===============
 
-.. _this tutorial: https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#closing
-
 """
 
 import numpy

diff --git a/cellprofiler/modules/dilateimage.py b/cellprofiler/modules/dilateimage.py
@@ -2,7 +2,7 @@
 DilateImage
 ===========
 
-**DilateImage** expands bright shapes in an image. See `this tutorial`_ for more information.
+**DilateImage** expands bright shapes in an image. See `this tutorial <https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#dilation>`__ for more information.
 
 |
 
@@ -12,8 +12,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#dilation
-
 """
 
 from cellprofiler_core.module import ImageProcessing

diff --git a/cellprofiler/modules/erodeimage.py b/cellprofiler/modules/erodeimage.py
@@ -2,9 +2,9 @@
 
 """
 ErodeImage
-=======
+==========
 
-**ErodeImage** shrinks bright shapes in an image. See `this tutorial`_ for more information.
+**ErodeImage** shrinks bright shapes in an image. See `this tutorial <https://scikit-image.org/docs/stable/auto_examples/applications/plot_morphology.html#erosion>`__ for more information.
 
 |
 
@@ -14,8 +14,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: https://scikit-image.org/docs/stable/auto_examples/applications/plot_morphology.html#erosion
-
 """
 
 from cellprofiler_core.module import ImageProcessing

diff --git a/cellprofiler/modules/medialaxis.py b/cellprofiler/modules/medialaxis.py
@@ -5,7 +5,7 @@
 **MedialAxis** computes the medial axis or topological skeleton of a binary image. Rather than by sequentially
 removing pixels as in **MorphologicalSkeleton**, the medial axis is computed based on the 
 distance transform of the thresholded image (i.e., the distance each foreground pixel is 
-from a background pixel). See `this tutorial`_ for more information. 
+from a background pixel). See `this tutorial <http://scikit-image.org/docs/dev/auto_examples/edges/plot_skeleton.html>`__ for more information. 
 
 |
 
@@ -15,7 +15,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: http://scikit-image.org/docs/dev/auto_examples/edges/plot_skeleton.html
 """
 
 import numpy

diff --git a/cellprofiler/modules/morphologicalskeleton.py b/cellprofiler/modules/morphologicalskeleton.py
@@ -2,7 +2,7 @@
 MorphologicalSkeleton
 =====================
 
-**MorphologicalSkeleton** thins an image into a single-pixel wide skeleton. See `this tutorial`_ for more information.
+**MorphologicalSkeleton** thins an image into a single-pixel wide skeleton. See `this tutorial <https://scikit-image.org/docs/0.14.x/auto_examples/xx_applications/plot_morphology.html#skeletonize>`__ for more information.
 
 |
 
@@ -12,8 +12,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: https://scikit-image.org/docs/0.14.x/auto_examples/xx_applications/plot_morphology.html#skeletonize
-
 """
 
 import skimage.morphology

diff --git a/cellprofiler/modules/opening.py b/cellprofiler/modules/opening.py
@@ -4,7 +4,7 @@
 
 **Opening** is the dilation of the erosion of an image. It’s used to
 remove salt noise (small bright spots) and connect small dark cracks. 
-See `this tutorial`_ for more information.
+See `this tutorial <https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#opening>`__ for more information.
 
 |
 
@@ -14,8 +14,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: https://scikit-image.org/docs/dev/auto_examples/applications/plot_morphology.html#opening
-
 """
 
 import numpy

diff --git a/cellprofiler/modules/reducenoise.py b/cellprofiler/modules/reducenoise.py
@@ -7,7 +7,7 @@
 as in **GaussianFilter**, multiple neighborhoods are pooled together. The
 neighborhood pool is determined by scanning the image for regions similar to
 the area around the central pixel using a correlation metric and a cutoff value.
-See `this tutorial`_ for more information.
+See `this tutorial <http://scikit-image.org/docs/dev/auto_examples/filters/plot_nonlocal_means.html>`__ for more information.
 
 |
 
@@ -17,7 +17,6 @@
 YES          YES          NO
 ============ ============ ===============
 
-.. _this tutorial: http://scikit-image.org/docs/dev/auto_examples/filters/plot_nonlocal_means.html
 """
 
 import skimage.restoration

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,6 +22,7 @@
 import sphinx_rtd_theme
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))
+sys.path.insert(0,os.path.abspath(os.path.join("..","..","..","core")))
 
 
 # -- General configuration ------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -65,6 +65,11 @@ References
 
 For a full list of references, visit our `citation`_ page.
 
+-  McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW,
+   Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W. (2018)
+   "CellProfiler 3.0: Next-generation image processing for biology."
+   *PLoS biology* 16(7), e2005970
+   (`link <https://doi.org/10.1371/journal.pbio.2005970>`__)
 -  Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O,
    Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM
    (2006) “CellProfiler: image analysis software for identifying and
@@ -212,11 +217,22 @@ in a future version of CellProfiler.
    :caption: Legacy Features
    :titlesonly:
 
-   help/legacy_load_modules
    help/legacy_matlab_image
 
 `(Jump to top)`_
 
 :ref:`search`
 
 .. _(Jump to top): index.html#
+
+License
+=======
+
+.. toctree::
+   :caption: License
+
+   modules/license
+
+:ref:`search`
+
+.. _(Jump to top): index.html#
diff --git a/docs/source/modules/advanced.rst b/docs/source/modules/advanced.rst
@@ -16,31 +16,33 @@ Advanced modules include computer vision algorithms.
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.erosion
+.. automodule:: cellprofiler.modules.erodeimage
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.fillobjects
+.. automodule:: cellprofiler.modules.erodeobjects
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.gaussianfilter
+
+.. automodule:: cellprofiler.modules.fillobjects
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.label
+.. automodule:: cellprofiler.modules.gaussianfilter
 
 `(Jump to top)`_
 
+
 .. automodule:: cellprofiler.modules.matchtemplate
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.medianfilter
+.. automodule:: cellprofiler.modules.medialaxis
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.medialaxis
+.. automodule:: cellprofiler.modules.medianfilter
 
 `(Jump to top)`_
 
@@ -60,10 +62,6 @@ Advanced modules include computer vision algorithms.
 
 `(Jump to top)`_
 
-.. automodule:: cellprofiler.modules.removeobjectsbysize
-
-`(Jump to top)`_
-
 .. automodule:: cellprofiler.modules.shrinktoobjectcenters
 
 `(Jump to top)`_

diff --git a/docs/source/modules/imageprocessing.rst b/docs/source/modules/imageprocessing.rst
@@ -4,7 +4,7 @@ Image Processing
 ----------------
 Image Processing modules apply an operation to an image and output a new image.
 
-.. automodule:: cellprofiler.modules.align
+.. automodule:: cellprofiler_core.modules.align
 
 `(Jump to top)`_
 

diff --git a/docs/source/modules/objectprocessing.rst b/docs/source/modules/objectprocessing.rst
@@ -9,6 +9,14 @@ have been identified in an image.
 
 `(Jump to top)`_
 
+.. automodule:: cellprofiler.modules.combineobjects
+
+`(Jump to top)`_
+
+.. automodule:: cellprofiler.modules.convertimagetoobjects
+
+`(Jump to top)`_
+
 .. automodule:: cellprofiler.modules.convertobjectstoimage
 
 `(Jump to top)`_
@@ -65,4 +73,4 @@ have been identified in an image.
 
 `(Jump to top)`_
 
-.. _(Jump to top): objectprocessing.html#
+.. _(Jump to top): objectprocessing.html#