Commit 83625255 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez Committed by jlaura
Browse files

CN refactor + bug fixes (#254) 

* removed cn class, bugfixes for jupyter tutorial

* formatting

* Improved cnet generation performence, added cnet masking

* updated notebooks with cnet work

* removed notebook checkpoints

* removed unused notebook

* removed some print statements and a spatial suppression bug

* updated notebooks

* removed functions that were originally in the ControlNetwork class, they are no longer needed after the refactor
parent 2442512f

autocnet/control/control.py

+15 −131
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ from autocnet.matcher import subpixel as sp 


from plio.io.io_controlnetwork import to_isis, write_filelist





def subpixel_match(cg, cn, threshold=0.9, template_size=19, search_size=53, max_x_shift=1.0, max_y_shift=1.0, **kwargs):



    def subpixel_group(group, threshold=0.9, template_size=19, search_size=53, max_x_shift=1.0, max_y_shift=1.0, **kwargs):
@@ -28,12 +29,17 @@ def subpixel_match(cg, cn,threshold=0.9, template_size=19, search_size=53, max_x 
            d_search = sp.clip_roi(d_img, (r.x, r.y), search_size)

            #d_search = cv2.Canny(bytescale(d_search), 50,100)



            xoff,yoff,corr = sp.subpixel_offset(s_template, d_search, **kwargs)

            xoff, yoff, corr = sp.subpixel_offset(

                s_template, d_search, **kwargs)

            offs.append([xoff, yoff, corr])

        df = pd.DataFrame(offs, columns=['x_off', 'y_off', 'corr'], index=group.index)

        df = pd.DataFrame(

            offs, columns=['x_off', 'y_off', 'corr'], index=group.index)

        return df

    gps = cn.data.groupby('point_id').apply(subpixel_group,threshold=0.9,max_x_shift=5, max_y_shift=5,template_size=template_size, search_size=search_size,**kwargs)

    cn.data[['x_off', 'y_off', 'corr']] = gps.reset_index()[['x_off', 'y_off', 'corr']]

    gps = cn.data.groupby('point_id').apply(subpixel_group, threshold=0.9, max_x_shift=5,

                                            max_y_shift=5, template_size=template_size, search_size=search_size, **kwargs)

    cn.data[['x_off', 'y_off', 'corr']] = gps.reset_index()[

        ['x_off', 'y_off', 'corr']]





def identify_potential_overlaps(cg, cn, overlap=True):

    """
@@ -56,7 +62,6 @@ def identify_potential_overlaps(cg, cn, overlap=True): 
                        for a new point.

    """





    fc = cg.compute_fully_connected_components()



    candidate_cliques = []
@@ -82,7 +87,8 @@ def identify_potential_overlaps(cg, cn, overlap=True): 
        # Determine whether a 'real' lat/lon are to be used and reproject

        if overlap:

            row = p.iloc[0]

            lat, lon = cg.node[row.image_index]['data'].geodata.pixel_to_latlon(row.x, row.y)

            lat, lon = cg.node[row.image_index]['data'].geodata.pixel_to_latlon(

                row.x, row.y)

        else:

            lat, lon = 0, 0
@@ -91,7 +97,6 @@ def identify_potential_overlaps(cg, cn, overlap=True): 
        candidate_cliques.append([uncovered, cycle_to_punch])

        idx.append(i)





    candidate_cliques = gpd.GeoDataFrame(candidate_cliques, index=idx,

                                         columns=['candidates', 'subgraph'], geometry=geoms)
@@ -104,7 +109,8 @@ def identify_potential_overlaps(cg, cn, overlap=True): 
        """

        cycle_to_punch = group.subgraph.iloc[0]

        subgraph = cg.create_node_subgraph(cycle_to_punch)

        union, _ = subgraph.compute_intersection(cycle_to_punch[0])#.query('overlaps_all == True')

        union, _ = subgraph.compute_intersection(

            cycle_to_punch[0])  # .query('overlaps_all == True')

        intersection = group.intersects(union.unary_union)

        return intersection
@@ -118,128 +124,6 @@ def identify_potential_overlaps(cg, cn, overlap=True): 
    else:

        return candidate_cliques.candidates



def deepen_correspondences(cg, cn):

    pass



class ControlNetwork(object):

    measures_keys = ['point_id', 'image_index', 'keypoint_index', 'edge', 'match_idx', 'x', 'y', 'x_off', 'y_off', 'corr', 'valid']



    def __init__(self):

        self._point_id = 0

        self._measure_id = 0

        self.measure_to_point = {}

        self.data = pd.DataFrame(columns=self.measures_keys)



    @classmethod

    def from_candidategraph(cls, matches):

        cls = ControlNetwork()

        for match in matches:

            for idx, row in match.iterrows():

                edge = (row.source_image, row.destination_image)

                source_key = (row.source_image, row.source_idx)

                source_fields = row[['source_x', 'source_y']]

                destin_key = (row.destination_image, row.destination_idx)

                destin_fields = row[['destination_x', 'destination_y']]

                if cls.measure_to_point.get(source_key, None) is not None:

                    tempid = cls.measure_to_point[source_key]

                    cls.add_measure(destin_key, edge, row.name, destin_fields, point_id=tempid)

                elif cls.measure_to_point.get(destin_key, None) is not None:

                    tempid = cls.measure_to_point[destin_key]

                    cls.add_measure(source_key, edge, row.name,  source_fields, point_id=tempid)

                else:

                    cls.add_measure(source_key, edge, row.name,  source_fields)

                    cls.add_measure(destin_key, edge,row.name,  destin_fields)

                    cls._point_id += 1



        cls.data.index.name = 'measure_id'

        return cls



    def add_measure(self, key, edge, match_idx, fields, point_id=None):

        """

        Create a new measure that is coincident to a given point.  This method does not

        create the point if is missing.  When a measure is added to the graph, an associated

        row is added to the measures dataframe.



        Parameters

        ----------

        key : hashable

                  Some hashable id.  In the case of an autocnet graph object the

                  id should be in the form (image_id, match_id)



        point_id : hashable

                   The point to link the node to.  This is most likely an integer, but

                   any hashable should work.

        """

        if key in self.measure_to_point.keys():

            return

        if point_id == None:

            point_id = self._point_id

        self.measure_to_point[key] = point_id

        # The node_id is a composite key (image_id, correspondence_id), so just grab the image

        image_id = key[0]

        match_id = key[1]

        self.data.loc[self._measure_id] = [point_id, image_id, match_id, edge, match_idx, *fields, 0, 0, np.inf, True]

        self._measure_id += 1



    def remove_measure(self, idx):

        self.data = self.data.drop(self.data.index[idx])

        for r in idx:

            self.measure_to_point.pop(r, None)



    def validate_points(self):

        """

        Ensure that all control points currently in the nework are valid.



        Criteria for validity:



          * Singularity: A control point can have one and only one measure from any image



        Returns

        -------

         : pd.Series



        """



        def func(g):

            # One and only one measure constraint

            if g.image_index.duplicated().any():

                return True

            else: return False

        return self.data.groupby('point_id').apply(func)



    def clean_singles(self):

        """

        Take the `data` dataframe and return only those points with

        at least two measures.  This is automatically called before writing

        as functions such as subpixel matching can result in orphaned measures.

        """

        return self.data.groupby('point_id').apply(lambda g: g if len(g) > 1 else None)



    def to_isis(self, outname, serials, olist, *args, **kwargs): #pragma: no cover

        """

        Write the control network out to the ISIS3 control network format.

        """



        if self.validate_points().any() == True:

            warnings.warn('Control Network is not ISIS3 compliant.  Please run the validate_points method on the control network.')

            return



        # Apply the subpixel shift

        self.data.x += self.data.x_off

        self.data.y += self.data.y_off



        to_isis(outname + '.net', self.data.query('valid == True'),

                serials, *args, **kwargs)

        write_filelist(olist, outname + '.lis')



        # Back out the subpixel shift

        self.data.x -= self.data.x_off

        self.data.y -= self.data.y_off



    def to_bal(self):

        """

        Write the control network out to the Bundle Adjustment in the Large

        (BAL) file format.  For more information see:

        http://grail.cs.washington.edu/projects/bal/

        """

def deepen_correspondences(cg, cn):

    pass

autocnet/graph/edge.py

+4 −1
Original line number Diff line number Diff line
@@ -56,6 +56,7 @@ class Edge(dict, MutableMapping): 
        self['destin_mbr'] = None

        self['overlap_latlon_coords'] = None





    def __repr__(self):

        return """

        Source Image Index: {}
@@ -63,10 +64,12 @@ class Edge(dict, MutableMapping): 
        Available Masks: {}

        """.format(self.source, self.destination, self.masks)





    def __eq__(self, other):

        return utils.compare_dicts(self.__dict__, other.__dict__) *\

               utils.compare_dicts(self, other)





    @property

    def matches(self):

        if not hasattr(self, '_matches'):
@@ -487,7 +490,7 @@ class Edge(dict, MutableMapping): 
            self.costs.loc[mask, 'correlation'] = strengths





    def suppress(self, suppression_func=spf.correlation, clean_keys=[], maskname='suppression', **kwargs):

    def suppress(self, suppression_func=spf.distance, clean_keys=[], maskname='suppression', **kwargs):

        """

        Apply a disc based suppression algorithm to get a good spatial

        distribution of high quality points, where the user defines some

autocnet/graph/network.py

+230 −57

File changed.

Preview size limit exceeded, changes collapsed.

autocnet/graph/node.py

+0 −1
Original line number Diff line number Diff line
@@ -18,7 +18,6 @@ from autocnet.io import keypoints as io_keypoints 
from autocnet.matcher.add_depth import deepen_correspondences

from autocnet.matcher import cpu_extractor as fe

from autocnet.matcher import cpu_outlier_detector as od

from autocnet.matcher import suppression_funcs as spf

from autocnet.cg.cg import convex_hull_ratio



from autocnet.vis.graph_view import plot_node

autocnet/matcher/cpu_outlier_detector.py

+1 −1
Original line number Diff line number Diff line
@@ -45,7 +45,7 @@ def distance_ratio(edge, matches, ratio=0.8, single=False): 
    return mask





def spatial_suppression(df, bounds, xkey='lon', ykey='lat', k=60, error_k=0.05, nsteps=250):

def spatial_suppression(df, bounds, xkey='x', ykey='y', k=60, error_k=0.05, nsteps=250):

    """

    Apply the spatial suppression algorithm over an arbitrary domain for all of the spatial

    data in the provided data frame.