Commit 74799fdc authored by Adoram-Kershner, Lauren's avatar Adoram-Kershner, Lauren
Browse files

Merge branch 'docs' into 'main' 

fixes: documentation env solve and build

See merge request astrogeology/autocnet!645
parents a88339d4 2b489137

autocnet/cg/change_detection.py

+1 −1
Original line number Original line Diff line number Diff line
@@ -538,7 +538,7 @@ def rv_detector(im1, im2, search_size, pattern_size=None, threshold=.999): 
    RV coefficient based change detection. This computes an RV coefficient on a sliding window 

    RV coefficient based change detection. This computes an RV coefficient on a sliding window 

    and correlates low scores below the input threshold to expected change.  

    and correlates low scores below the input threshold to expected change.  

    

    

    **WARNING*: The time complexity for this is `1 + (search_size - pattern_size))^2` per overlapping pixel between im1 and im2. So larger the differemce between the search and pattern size, it causes compute time to increase exponentially. 

    **WARNING**: The time complexity for this is `1 + (search_size - pattern_size))^2` per overlapping pixel between im1 and im2. So larger the differemce between the search and pattern size, it causes compute time to increase exponentially. 





    Parameters

    Parameters

    ----------

    ----------

autocnet/graph/edge.py

+5 −5
Original line number Original line Diff line number Diff line
@@ -394,7 +394,8 @@ class Edge(dict, MutableMapping): 




    def compute_homography(self, method='ransac', clean_keys=[], pid=None, maskname='homography', **kwargs):

    def compute_homography(self, method='ransac', clean_keys=[], pid=None, maskname='homography', **kwargs):

        """

        """

        For each edge in the (sub) graph, compute the homography

        For each edge in the (sub) graph, compute the homography.



        Parameters

        Parameters

        ----------

        ----------

        outlier_algorithm : object

        outlier_algorithm : object
@@ -1264,9 +1265,8 @@ class NetworkEdge(Edge): 




        Parameters

        Parameters

        ----------

        ----------

        outlier_method: str

        outlier_method: {'IQR',}

                        method used to determine outliers.

                        method used to determine outliers. Options are: 

                        Current methods:

                          - interquartile range ('IQR') of line/sample shift

                          - interquartile range ('IQR') of line/sample shift





        Returns

        Returns

autocnet/graph/network.py

+18 −9
Original line number Original line Diff line number Diff line
@@ -1000,6 +1000,8 @@ class CandidateGraph(nx.Graph): 
        """

        """

        Computes a voronoi weight for each edge in a given graph.

        Computes a voronoi weight for each edge in a given graph.

        Can function as is, but is slightly optimized for complete subgraphs.

        Can function as is, but is slightly optimized for complete subgraphs.



        Parameters

        ----------

        ----------

        kwargs : dict

        kwargs : dict

                      keyword arguments that get passed to compute_voronoi

                      keyword arguments that get passed to compute_voronoi
@@ -2226,21 +2228,24 @@ class NetworkCandidateGraph(CandidateGraph): 
        -----

        -----

        Here, we provide usage examples for a few, potentially common use cases.

        Here, we provide usage examples for a few, potentially common use cases.





        ## Spatial Query

        Spatial Query

        =============

        This example selects those images that intersect a given bounding polygon.  The polygon is

        This example selects those images that intersect a given bounding polygon.  The polygon is

        specified as a Well Known Text LINESTRING with the first and last points being the same.

        specified as a Well Known Text LINESTRING with the first and last points being the same.

        The query says, select the geom (the bounding polygons in the database) that

        The query says, select the geom (the bounding polygons in the database) that

        intersect the user provided polygon (the LINESTRING) in the given spatial reference system

        intersect the user provided polygon (the LINESTRING) in the given spatial reference system

        (SRID), 949900.

        (SRID), 949900. ::





            SELECT * FROM Images WHERE ST_INTERSECTS(geom, ST_Polygon(ST_GeomFromText('LINESTRING(159 10, 159 11, 160 11, 160 10, 159 10)'),949900)) = TRUE

            SELECT * FROM Images WHERE ST_INTERSECTS(geom, ST_Polygon(ST_GeomFromText('LINESTRING(159 10, 159 11, 160 11, 160 10, 159 10)'),949900)) = TRUE





        ## Select from a specific orbit

        Select from a specific orbit

        ============================

        This example selects those images that are from a particular orbit. In this case,

        This example selects those images that are from a particular orbit. In this case,

        the regex string pulls all P##_* orbits and creates a graph from them. This method

        the regex string pulls all P##_* orbits and creates a graph from them. This method

        does not guarantee that the graph is fully connected.

        does not guarantee that the graph is fully connected. ::





          SELECT * FROM Images WHERE (split_part(path, '/', 6) ~ 'P[0-9]+_.+') = True

          SELECT * FROM Images WHERE (split_part(path, '/', 6) ~ 'P[0-9]+_.+') = True



        """

        """





        composite_query = '''WITH i as ({}) SELECT i1.id

        composite_query = '''WITH i as ({}) SELECT i1.id
@@ -2647,6 +2652,7 @@ class NetworkCandidateGraph(CandidateGraph): 
        distirbute_points_kwargs : dict

        distirbute_points_kwargs : dict

                                   Of arguments that are passed on the the

                                   Of arguments that are passed on the the

                                   distribute_points_in_geom argument in autocnet.cg.cg

                                   distribute_points_in_geom argument in autocnet.cg.cg

        

        Returns

        Returns

        -------

        -------

        valid : np.ndarray

        valid : np.ndarray
@@ -2655,7 +2661,8 @@ class NetworkCandidateGraph(CandidateGraph): 
        Examples

        Examples

        --------

        --------

        To use this method, one can first define the spacing of ground points in the north-

        To use this method, one can first define the spacing of ground points in the north-

        south and east-west directions using the `distribute_points_kwargs` keyword argument:

        south and east-west directions using the `distribute_points_kwargs` keyword argument::



            def ns(x):

            def ns(x):

                from math import ceil

                from math import ceil

                return ceil(round(x,1)*3)

                return ceil(round(x,1)*3)
@@ -2663,16 +2670,18 @@ class NetworkCandidateGraph(CandidateGraph): 
                from math import ceil

                from math import ceil

                return ceil(round(x,1)*3)

                return ceil(round(x,1)*3)





        Next these arguments can be passed in in order to generate the grid of points:

        Next these arguments can be passed in in order to generate the grid of points::



            distribute_points_kwargs = {'nspts_func':ns, 'ewpts_func':ew, 'method':'classic'}

            distribute_points_kwargs = {'nspts_func':ns, 'ewpts_func':ew, 'method':'classic'}

            valid = ncg.distribute_ground_uniform(distribute_points_kwargs=distribute_points_kwargs)

            valid = ncg.distribute_ground_uniform(distribute_points_kwargs=distribute_points_kwargs)





        At this point, it is possible to visualize the valid points inside of a Jupyter notebook. This

        At this point, it is possible to visualize the valid points inside of a Jupyter notebook. This

        is frequently convenient when combined with the `ncg.union` property that displays the unioned

        is frequently convenient when combined with the `ncg.union` property that displays the unioned

        geometries in the NetworkCandidateGraph.

        geometries in the NetworkCandidateGraph.



        Finally, the valid points can be propagated using apply. The code below will use the defined base

        Finally, the valid points can be propagated using apply. The code below will use the defined base

        to find the most interesting ground feature in the region of the valid point and write that point

        to find the most interesting ground feature in the region of the valid point and write that point

        to the table defined by CandidateGroundPoints (autocnet.io.db.model):

        to the table defined by CandidateGroundPoints (autocnet.io.db.model)::





            base = 'mc11_oxia_palus_dir_final.cub'

            base = 'mc11_oxia_palus_dir_final.cub'

            ncg.apply('matcher.ground.find_most_interesting_ground', on=valid, args=(base,))

            ncg.apply('matcher.ground.find_most_interesting_ground', on=valid, args=(base,))

autocnet/io/db/controlnetwork.py

+2 −1
Original line number Original line Diff line number Diff line
@@ -44,10 +44,12 @@ ORDER BY measures."pointid", measures."id"; 
        """

        """

        Given a set of points/measures in an autocnet database, generate an ISIS

        Given a set of points/measures in an autocnet database, generate an ISIS

        compliant control network.

        compliant control network.



        Parameters

        Parameters

        ----------

        ----------

        path : str

        path : str

               The full path to the output network.

               The full path to the output network.



        flistpath : str

        flistpath : str

                    (Optional) the path to the output filelist. By default

                    (Optional) the path to the output filelist. By default

                    the outout filelist path is genrated programatically

                    the outout filelist path is genrated programatically
@@ -56,7 +58,6 @@ ORDER BY measures."pointid", measures."id"; 
        sql : str

        sql : str

              The sql query to execute in the database.

              The sql query to execute in the database.

        """

        """

        print(sql)

        

        

        df = pd.read_sql(sql, engine)

        df = pd.read_sql(sql, engine)

autocnet/matcher/cpu_decompose.py

+3 −2
Original line number Original line Diff line number Diff line
@@ -9,7 +9,7 @@ from autocnet.transformation.decompose import coupled_decomposition 
def decompose_and_match(self, k=2, maxiteration=3, size=18, buf_dist=3, **kwargs):

def decompose_and_match(self, k=2, maxiteration=3, size=18, buf_dist=3, **kwargs):

    """

    """

    Similar to match, this method first decomposed the image into

    Similar to match, this method first decomposed the image into

    $4^{maxiteration}$ subimages and applys matching between each sub-image.

    $4^{maxiteration}$ subimages and applies matching between each sub-image.





    This method is potential slower than the standard match due to the

    This method is potential slower than the standard match due to the

    overhead in matching, but can be significantly more accurate.  The

    overhead in matching, but can be significantly more accurate.  The
@@ -28,7 +28,7 @@ def decompose_and_match(self, k=2, maxiteration=3, size=18, buf_dist=3, **kwargs 
    maxiteration : int

    maxiteration : int

                   When using coupled decomposition, the number of recursive

                   When using coupled decomposition, the number of recursive

                   divisions to apply.  The total number of resultant

                   divisions to apply.  The total number of resultant

                   sub-images will be 4 ** maxiteration.  Approximate values:

                   sub-images will be 4 ** maxiteration.  Approximate values::





                    | Number of megapixels | maxiteration |

                    | Number of megapixels | maxiteration |

                    |----------------------|--------------|

                    |----------------------|--------------|
@@ -49,6 +49,7 @@ def decompose_and_match(self, k=2, maxiteration=3, size=18, buf_dist=3, **kwargs 
               the (sub)image a point must be in order to be used as a

               the (sub)image a point must be in order to be used as a

               partioning point.  The smaller the distance, the more likely

               partioning point.  The smaller the distance, the more likely

               percision errors can results in erroneous partitions.

               percision errors can results in erroneous partitions.



    """

    """

    def func(group):

    def func(group):

        ratio = 0.8

        ratio = 0.8