Switching over to new filenames

Author: cindygr

.DS_Store

@@ -13,7 +13,12 @@
 from os.path import exists
 import json
 from line_seg_2d import LineSeg2D
-from HandleFileNames import HandleFileNames
+
+from os.path import abspath as os_abs_path
+from sys import path as syspath
+syspath.insert(0, os_abs_path('../Utilities'))
+syspath.insert(0, os_abs_path('./Utilities'))
+from FileNames import FileNames
 
 
 class BaseStatsImage:
@@ -47,7 +52,12 @@ def __init__(self, fname_mask_image, fname_calculated=None, fname_debug=None, b_
         @param b_recalc: Force recalculate the result, y/n"""
 
         self.stats_dict = None
-        mask_image_rgb = cv2.imread(fname_mask_image)
+        if exists(fname_mask_image):
+            mask_image_rgb = cv2.imread(fname_mask_image)
+        else:
+            self.mask_image = np.zeros((8, 8), dtype=np.uint8)
+            return
+        
         if len(mask_image_rgb.shape) == 3:
             self.mask_image = cv2.cvtColor(mask_image_rgb, cv2.COLOR_BGR2GRAY)
         else:
@@ -179,22 +189,43 @@ def debug_image(self, in_image):
         ymax = self.stats_dict["y_max"]
         LineSeg2D.draw_rect(in_image, [[xmin, xmax], [ymin, ymax]], (256, 128, 128), 2)
 
+    @staticmethod
+    def create_from_filenames(filenames, index=(0,0,0,0), b_do_recalc=False, b_do_debug=True):
+        """ Create a base image from a file name in FileNames
+        @param filenames - FileNames instance
+        @param index tuple (eg (0,0,0,0))
+        @param b_do_recalc - recalculate from scratch
+        @param b_do_debug - spit out a debug image y/n
+        @return base stats image"""
+
+        # File name
+        mask_fname = filenames.get_mask_name(index=index, b_add_tag=True)
+        # Debug image file name
+        if b_do_debug:
+            mask_fname_debug = filenames.get_mask_name(index=index, b_debug_path=True, b_add_tag=False)
+        else:
+            mask_fname_debug = None
+
+        # The stub of the filename to save all of the data to
+        mask_fname_calculate = filenames.get_mask_name(index=index, b_calculate_path=True, b_add_tag=False)
+
+        if not exists(mask_fname):
+            print(f"Warning, file {mask_fname} does not exist")
+        b_stats = BaseStatsImage(mask_fname, mask_fname_calculate, mask_fname_debug, b_recalc=b_do_recalc)
+        return b_stats
+
 
 if __name__ == '__main__':
+    path_bpd_envy = "/Users/cindygrimm/VSCode/treefitting/Image_based/data/EnvyTree/"
+    all_fnames_envy = FileNames.read_filenames(path=path_bpd_envy, 
+                                               fname="envy_fnames.json")
+    BaseStatsImage.create_from_filenames(all_fnames_envy, (0, 0, 0, 0), b_do_recalc=False, b_do_debug=False)
+
     #path_bpd = "./data/trunk_segmentation_names.json"
     path_bpd = "./data/forcindy_fnames.json"
-    all_files = HandleFileNames.read_filenames(path_bpd)
+    all_files = FileNames.read_filenames(path_bpd)
 
     b_do_debug = True
     b_do_recalc = False
     for ind in all_files.loop_masks():
-        mask_fname = all_files.get_mask_name(path=all_files.path, index=ind, b_add_tag=True)
-        mask_fname_debug = all_files.get_mask_name(path=all_files.path_debug, index=ind, b_add_tag=False)
-        if not b_do_debug:
-            mask_fname_debug = None
-
-        mask_fname_calculate = all_files.get_mask_name(path=all_files.path_calculated, index=ind, b_add_tag=False)
-
-        if not exists(mask_fname):
-            raise ValueError(f"Error, file {mask_fname} does not exist")
-        b_stats = BaseStatsImage(mask_fname, mask_fname_calculate, mask_fname_debug, b_recalc=b_do_recalc)
+        BaseStatsImage.create_from_filenames(all_files, ind, b_do_debug=b_do_debug, b_do_recalc=b_do_recalc)

Image_based/.DS_Store

@@ -0,0 +1 @@
+../../../../PycharmProjects/treefitting/Image_based/data/EnvyTree

Image_based/BaseStatsImage.py

@@ -12,8 +12,8 @@
 import json
 from os.path import exists
 from line_seg_2d import LineSeg2D
-from HandleFileNames import HandleFileNames
 from fit_bezier_cyl_2d_edge import FitBezierCyl2DEdge
+from FileNames import FileNames
 
 
 class ExtractCurves:
@@ -38,6 +38,10 @@ def __init__(self, fname_rgb_image, fname_edge_image, fname_mask_image, params=N
                                               params=params,
                                               fname_debug=fname_debug,
                                               b_recalc=b_recalc)
+        
+        if not exists(fname_mask_image):
+            self.params = None
+            return
 
         # List o pairs (t, plus/minus)
         self.left_curve = []
@@ -279,11 +283,50 @@ def curves_from_stats(stats_edge, params):
         # Left curve as t, perc pairs and same for right
         return crvs[0], crvs[1]
 
+    @staticmethod
+    def create_from_filenames(filenames, index=(0,0,0,0), b_do_recalc=False, b_do_debug=True, b_use_optical_flow_edge=False):
+        """ Create a base image from a file name in FileNames
+        @param filenames - FileNames instance
+        @param index tuple (eg (0,0,0,0))
+        @param b_do_recalc - recalculate from scratch
+        @param b_do_debug - spit out a debug image y/n
+        @param b_use_optical_flow_edge - use optical flow edge image instead of rgb edge image
+        @return extract curves"""
+
+        rgb_fname = filenames.get_image_name(index=index, b_add_tag=True)
+
+        if not exists(rgb_fname):
+            raise ValueError(f"No file {rgb_fname}")
+
+        # File name
+        mask_fname = filenames.get_mask_name(index=index, b_add_tag=True)
+        edge_fname = filenames.get_edge_name(index=index, b_optical_flow=b_use_optical_flow_edge, b_add_tag=True)
+        # Debug image file name
+        if b_do_debug:
+            mask_fname_debug = filenames.get_mask_name(index=index, b_debug_path=True, b_add_tag=False)
+        else:
+            mask_fname_debug = None
+
+        # The stub of the filename to save all of the data to
+        mask_fname_calculate = filenames.get_mask_name(index=index, b_calculate_path=True, b_add_tag=False)
+
+        if not exists(mask_fname):
+            print(f"Warning, file {mask_fname} does not exist")
+        profile_crvs = ExtractCurves(rgb_fname, edge_fname, mask_fname,
+                                     fname_calculated=mask_fname_calculate,
+                                     fname_debug=mask_fname_debug, b_recalc=b_do_recalc)
+        return profile_crvs
+
 
 if __name__ == '__main__':
+    path_bpd_envy = "/Users/cindygrimm/VSCode/treefitting/Image_based/data/EnvyTree/"
+    all_fnames_envy = FileNames.read_filenames(path=path_bpd_envy, 
+                                               fname="envy_fnames.json")
+    ExtractCurves.create_from_filenames(all_fnames_envy, (0, 0, 0, 0), b_do_recalc=False, b_do_debug=False)
+
     # path_bpd = "./data/trunk_segmentation_names.json"
     path_bpd = "./data/forcindy_fnames.json"
-    all_files = HandleFileNames.read_filenames(path_bpd)
+    all_files = FileNames.read_filenames(path_bpd)
 
     b_do_debug = True
     b_do_recalc = True

Image_based/data/EnvyTree

@@ -26,8 +26,8 @@
 from bezier_cyl_2d import BezierCyl2D
 from fit_bezier_cyl_2d import FitBezierCyl2D
 from line_seg_2d import LineSeg2D
-from HandleFileNames import HandleFileNames
 from fit_bezier_cyl_2d_mask import FitBezierCyl2DMask
+from FileNames import FileNames
 
 
 class FitBezierCyl2DEdge:
@@ -84,6 +84,10 @@ def __init__(self, fname_rgb_image, fname_edge_image, fname_mask_image, fname_ca
         #   This is the curve that will be fit to the edge
         self.bezier_crv_fit_to_edge = None
 
+        if not exists(fname_mask_image):
+            self.params = None
+            return
+
         # Copy params used in fit mask and add the new ones
         self.params = {}
         for k in self.mask_crv.params.keys():
@@ -424,28 +428,56 @@ def debug_image_edge_fit(self, image_debug):
         else:
             self.bezier_crv_fit_to_edge.draw_boundary(image_debug, 10)
 
+    @staticmethod
+    def create_from_filenames(filenames, index=(0,0,0,0), b_do_recalc=False, b_do_debug=True, b_use_optical_flow_edge=False):
+        """ Create a base image from a file name in FileNames
+        @param filenames - FileNames instance
+        @param index tuple (eg (0,0,0,0))
+        @param b_do_recalc - recalculate from scratch
+        @param b_do_debug - spit out a debug image y/n
+        @param b_use_optical_flow_edge - use optical flow edge image instead of rgb edge image        
+        @return FitBezierCyl2DEdge"""
+
+        rgb_fname = filenames.get_image_name(index=index, b_add_tag=True)
+
+        if not exists(rgb_fname):
+            raise ValueError(f"No file {rgb_fname}")
+
+        # File name
+        mask_fname = filenames.get_mask_name(index=index, b_add_tag=True)
+        # Debug image file name
+        if b_do_debug:
+            edge_fname_debug = filenames.get_mask_name(index=index, b_debug_path=True, b_add_tag=False)
+        else:
+            edge_fname_debug = None
+
+        edge_fname = filenames.get_edge_name(index=index, b_add_tag=True, b_optical_flow=b_use_optical_flow_edge)
+
+        # The stub of the filename to save all of the data to
+        edge_fname_calculate = filenames.get_mask_name(index=index, b_calculate_path=True, b_add_tag=False)
+
+        if not exists(mask_fname):
+            print(f"Warning, file {mask_fname} does not exist")
+        edge_crv = FitBezierCyl2DEdge(rgb_fname, edge_fname, mask_fname, edge_fname_calculate, edge_fname_debug, b_recalc=b_do_recalc)
+        return edge_crv
+
 
 if __name__ == '__main__':
+    path_bpd_envy = "/Users/cindygrimm/VSCode/treefitting/Image_based/data/EnvyTree/"
+    all_fnames_envy = FileNames.read_filenames(path=path_bpd_envy, 
+                                               fname="envy_fnames.json")
+    FitBezierCyl2DEdge.create_from_filenames(all_fnames_envy, (0, 0, 0, 0), b_do_recalc=False, b_do_debug=False)
+
     # path_bpd = "./data/trunk_segmentation_names.json"
     path_bpd = "./data/forcindy_fnames.json"
-    all_files = HandleFileNames.read_filenames(path_bpd)
+    all_files = FileNames.read_filenames(path_bpd)
 
     b_do_debug = True
     b_do_recalc = False
+    b_use_optical_flow = False
     for ind in all_files.loop_masks():
-        rgb_fname = all_files.get_image_name(path=all_files.path, index=ind, b_add_tag=True)
-        edge_fname = all_files.get_edge_image_name(path=all_files.path_calculated, index=ind, b_add_tag=True)
-        mask_fname = all_files.get_mask_name(path=all_files.path, index=ind, b_add_tag=True)
-        edge_fname_debug = all_files.get_mask_name(path=all_files.path_debug, index=ind, b_add_tag=False)
-        if not b_do_debug:
-            edge_fname_debug = None
-
-        edge_fname_calculate = all_files.get_mask_name(path=all_files.path_calculated, index=ind, b_add_tag=False)
-
-        if not exists(mask_fname):
-            raise ValueError(f"Error, file {mask_fname} does not exist")
-        if not exists(rgb_fname):
-            raise ValueError(f"Error, file {rgb_fname} does not exist")
-
-        edge_crv = FitBezierCyl2DEdge(rgb_fname, edge_fname, mask_fname, edge_fname_calculate, edge_fname_debug, b_recalc=b_do_recalc)
+        FitBezierCyl2DEdge.create_from_filenames(all_files, 
+                                                 b_do_debug=b_do_debug,
+                                                 b_do_recalc=b_do_recalc,
+                                                 b_use_optical_flow_edge=b_use_optical_flow)
     print("foo")

Image_based/extract_curves.py

@@ -17,7 +17,7 @@
 from bezier_cyl_2d import BezierCyl2D
 from fit_bezier_cyl_2d import FitBezierCyl2D
 from BaseStatsImage import BaseStatsImage
-from HandleFileNames import HandleFileNames
+from FileNames import FileNames
 
 
 class FitBezierCyl2DMask:
@@ -34,6 +34,10 @@ def __init__(self, fname_mask_image, fname_calculated=None, fname_debug=None, pa
         # First do the stats - this also reads the image in
         self.stats_dict = BaseStatsImage(fname_mask_image, fname_calculated, fname_debug, b_recalc)
 
+        if not exists(fname_mask_image):
+            self.params = None
+            return
+        
         # Now initialize bezier curve with info from stats - no need to cache this because it's so light-weight
         p0 = self.stats_dict.stats_dict["lower_left"]
         p2 = self.stats_dict.stats_dict["upper_right"]
@@ -202,24 +206,43 @@ def score_mask_fit(self, im_mask):
 
         return np.count_nonzero(pixs_in_both_masks) / np.count_nonzero(pixs_in_union)
 
+    @staticmethod
+    def create_from_filenames(filenames, index=(0,0,0,0), b_do_recalc=False, b_do_debug=True):
+        """ Create a base image from a file name in FileNames
+        @param filenames - FileNames instance
+        @param index tuple (eg (0,0,0,0))
+        @param b_do_recalc - recalculate from scratch
+        @param b_do_debug - spit out a debug image y/n
+        @return BezierCyl2DMask"""
+
+        # File name
+        mask_fname = filenames.get_mask_name(index=index, b_add_tag=True)
+        # Debug image file name
+        if b_do_debug:
+            mask_fname_debug = filenames.get_mask_name(index=index, b_debug_path=True, b_add_tag=False)
+        else:
+            mask_fname_debug = None
+
+        # The stub of the filename to save all of the data to
+        mask_fname_calculate = filenames.get_mask_name(index=index, b_calculate_path=True, b_add_tag=False)
+
+        if not exists(mask_fname):
+            print(f"Warning, file {mask_fname} does not exist")
+        b_crv_mask = FitBezierCyl2DMask(mask_fname, mask_fname_calculate, mask_fname_debug, b_recalc=b_do_recalc)
+        return b_crv_mask
+
 
 if __name__ == '__main__':
-    im = cv2.imread("/Users/grimmc/Downloads/depth_raw_3.jpg")
-    print(f" {im.min()}, {im.max()}")
+    path_bpd_envy = "/Users/cindygrimm/VSCode/treefitting/Image_based/data/EnvyTree/"
+    all_fnames_envy = FileNames.read_filenames(path=path_bpd_envy, 
+                                               fname="envy_fnames.json")
+    FitBezierCyl2DMask.create_from_filenames(all_fnames_envy, (0, 0, 0, 0), b_do_recalc=False, b_do_debug=False)
+
     # path_bpd = "./data/trunk_segmentation_names.json"
     path_bpd = "./data/forcindy_fnames.json"
-    all_files = HandleFileNames.read_filenames(path_bpd)
+    all_files = FileNames.read_filenames(path_bpd)
 
     b_do_debug = True
     b_do_recalc = False
     for ind in all_files.loop_masks():
-        mask_fname = all_files.get_mask_name(path=all_files.path, index=ind, b_add_tag=True)
-        mask_fname_debug = all_files.get_mask_name(path=all_files.path_debug, index=ind, b_add_tag=False)
-        if not b_do_debug:
-            mask_fname_debug = None
-
-        mask_fname_calculate = all_files.get_mask_name(path=all_files.path_calculated, index=ind, b_add_tag=False)
-
-        if not exists(mask_fname):
-            raise ValueError(f"Error, file {mask_fname} does not exist")
-        b_stats = FitBezierCyl2DMask(mask_fname, mask_fname_calculate, mask_fname_debug, b_recalc=b_do_recalc)
+        FitBezierCyl2DMask.create_from_filenames(all_files, ind, b_do_debug=b_do_debug, b_do_recalc=b_do_recalc)