update sphinx documentation

fish-quant · Jan 25, 2022 · ede24a7 · ede24a7
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diff --git a/docs/source/classification/features.rst b/docs/source/classification/features.rst
@@ -5,8 +5,8 @@ Features engineering
 
 .. currentmodule:: bigfish.classification
 
-Input coordinates preparation
-=============================
+Prepare input coordinates
+=========================
 
 Format input coordinates and compute intermediary results to prepare features
 computation:

diff --git a/docs/source/detection/spots.rst b/docs/source/detection/spots.rst
@@ -44,9 +44,11 @@ that limits the possibility to scale a spot detection. Our method includes a
 heuristic function to to automatically set this threshold:
 
 * :func:`bigfish.detection.automated_threshold_setting`
+* :func:`bigfish.detection.get_breaking_point`
 * :func:`bigfish.detection.get_elbow_values`
 
 .. autofunction:: automated_threshold_setting
+.. autofunction:: get_breaking_point
 .. autofunction:: get_elbow_values
 
 ------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -122,9 +122,6 @@ API reference
 
    utils/utils
 
-* :ref:`Utility functions<utils overview>`: Sanity checks, get constant values,
-  compute hash, save plots, etc...
-
 ------------
 
 Support

diff --git a/docs/source/plot/plot_detection.rst b/docs/source/plot/plot_detection.rst
@@ -1,7 +1,7 @@
 .. _plot_detection overview:
 
-Detection plots
-***************
+Detection plot
+**************
 
 .. currentmodule:: bigfish.plot
 

diff --git a/docs/source/plot/plot_image.rst b/docs/source/plot/plot_image.rst
@@ -1,7 +1,7 @@
 .. _plot_image overview:
 
-Field of view plots
-*******************
+Field of view plot
+******************
 
 .. currentmodule:: bigfish.plot
 

diff --git a/docs/source/plot/plot_segmentation.rst b/docs/source/plot/plot_segmentation.rst
@@ -1,7 +1,7 @@
 .. _plot_segmentation overview:
 
-Segmentation plots
-******************
+Segmentation plot
+*****************
 
 .. currentmodule:: bigfish.plot
 

diff --git a/docs/source/segmentation/postprocessing.rst b/docs/source/segmentation/postprocessing.rst
@@ -20,18 +20,13 @@ Clean segmentation results:
 * :func:`bigfish.segmentation.clean_segmentation`
 * :func:`bigfish.segmentation.remove_disjoint`
 
-Match nuclei and cells:
-
-* :func:`bigfish.segmentation.match_nuc_cell`
-
 See an example of application `here <https://github.com/fish-quant/big-fish-
 examples/blob/master/notebooks/4%20-%20Segment%20nuclei%20and%20cells.ipynb>`_.
 
 .. autofunction:: label_instances
 .. autofunction:: merge_labels
 .. autofunction:: clean_segmentation
 .. autofunction:: remove_disjoint
-.. autofunction:: match_nuc_cell
 
 ------------
 
@@ -48,4 +43,15 @@ Compute statistics for each segmented instance:
 .. autofunction:: compute_mean_diameter
 .. autofunction:: compute_mean_convexity_ratio
 .. autofunction:: compute_surface_ratio
-.. autofunction:: count_instances
+.. autofunction:: count_instances
+
+------------
+
+Match cells and nuclei
+======================
+
+.. currentmodule:: bigfish.multistack
+
+Match nuclei and cells:
+
+.. autofunction:: match_nuc_cell
diff --git a/docs/source/utils/utils.rst b/docs/source/utils/utils.rst
@@ -57,20 +57,18 @@ Compute moving average
 
 ------------
 
-Spot detection utilities
-========================
+Convert pixels and nanometers
+=============================
 
 .. currentmodule:: bigfish.detection
 
 * :func:`bigfish.detection.convert_spot_coordinates`
 * :func:`bigfish.detection.get_object_radius_pixel`
 * :func:`bigfish.detection.get_object_radius_nm`
-* :func:`bigfish.detection.get_breaking_point`
 
 .. autofunction:: convert_spot_coordinates
 .. autofunction:: get_object_radius_pixel
 .. autofunction:: get_object_radius_nm
-.. autofunction:: get_breaking_point
 
 ------------
-Original file line number
+Diff line change
@@ Expand Up / @@ -122,9 +122,6 @@ API reference @@
        utils/utils
-    * :ref:`Utility functions<utils overview>`: Sanity checks, get constant values,
-      compute hash, save plots, etc...
     ------------
     Support
@@ Expand Down @@