Merge pull request #37 from 20treeAI/remove_cfg_imports

Remove cfg imports

s2p/__init__.py

@@ -129,7 +129,7 @@ def pointing_correction(tile, i, cfg):
     A, m = pointing_accuracy.compute_correction(
         img1, img2, rpc1, rpc2, x, y, w, h, method,
         cfg['sift_match_thresh'], cfg['max_pointing_error'], cfg['matching_method'],
-        cfg['min_value'], cfg['max_value'], cfg['confidence_threshold']
+        cfg['min_value'], cfg['max_value'], cfg['confidence_threshold'], cfg
     )
 
     if A is not None:  # A is the correction matrix
@@ -142,7 +142,7 @@ def pointing_correction(tile, i, cfg):
             visualisation.plot_matches(img1, img2, rpc1, rpc2, m,
                                        os.path.join(out_dir,
                                                     'sift_matches_pointing.png'),
-                                       x, y, w, h)
+                                       x, y, w, h, cfg)
 
 
 def global_pointing_correction(cfg, tiles):
@@ -212,10 +212,14 @@ def rectification_pair(tile, i, cfg):
     H1, H2, disp_min, disp_max = rectification.rectify_pair(img1, img2,
                                                             rpc1, rpc2,
                                                             x, y, w, h,
-                                                            rect1, rect2, A, m,
+                                                            rect1, rect2, 
+                                                            cfg,
+                                                            A=A, 
+                                                            sift_matches=m,
                                                             method=cfg['rectification_method'],
                                                             hmargin=cfg['horizontal_margin'],
-                                                            vmargin=cfg['vertical_margin'])
+                                                            vmargin=cfg['vertical_margin'],
+                                                            )
 
     np.savetxt(os.path.join(out_dir, 'H_ref.txt'), H1, fmt='%12.6f')
     np.savetxt(os.path.join(out_dir, 'H_sec.txt'), H2, fmt='%12.6f')
@@ -246,7 +250,7 @@ def stereo_matching(tile, i, cfg):
     disp_min, disp_max = np.loadtxt(os.path.join(out_dir, 'disp_min_max.txt'))
 
     block_matching.compute_disparity_map(rect1, rect2, disp, mask,
-                                         cfg['matching_algorithm'], disp_min,
+                                         cfg['matching_algorithm'], cfg, disp_min,
                                          disp_max, timeout=cfg['mgm_timeout'],
                                          max_disp_range=cfg['max_disp_range'])
 
@@ -335,7 +339,7 @@ def disparity_to_ply(tile, cfg):
         with rasterio.open(os.path.join(out_dir, 'pair_1', 'rectified_ref.tif')) as f:
             ww, hh = f.width, f.height
 
-        colors = common.tmpfile(".tif")
+        colors = common.tmpfile(cfg['temporary_dir'], ".tif")
         success_state = common.image_apply_homography(colors, cfg['images'][0]['clr'],
                                       np.loadtxt(H_ref), ww, hh)
         if success_state is False:
@@ -450,7 +454,7 @@ def heights_fusion(cfg, tile):
     # merge the height maps (applying mean offset to register)
     fusion.merge_n(os.path.join(tile_dir, 'height_map.tif'), height_maps,
                    global_mean_heights, averaging=cfg['fusion_operator'],
-                   threshold=cfg['fusion_thresh'])
+                   threshold=cfg['fusion_thresh'], debug=cfg['debug'])
 
     if cfg['clean_intermediate']:
         for f in height_maps:
@@ -729,7 +733,7 @@ def main(user_cfg, start_from=0, merge_matches=False):
     common.print_elapsed_time()
 
     # cleanup
-    common.garbage_cleanup()
+    common.garbage_cleanup(cfg['clean_tmp'])
     common.print_elapsed_time(since_first_call=True)
 
 

s2p/block_matching.py

@@ -8,14 +8,13 @@
 import rasterio
 
 from s2p import common
-from s2p.config import cfg
 
 
 class MaxDisparityRangeError(Exception):
     pass
 
 
-def create_rejection_mask(disp, im1, im2, mask):
+def create_rejection_mask(disp, im1, im2, mask, temporary_dir):
     """
     Create rejection mask (0 means rejected, 1 means accepted)
     Keep only the points that are matched and present in both input images
@@ -25,14 +24,14 @@ def create_rejection_mask(disp, im1, im2, mask):
         im1, im2: rectified stereo pair
         mask: path to the output rejection mask
     """
-    tmp1 = common.tmpfile('.tif')
-    tmp2 = common.tmpfile('.tif')
+    tmp1 = common.tmpfile(temporary_dir, '.tif')
+    tmp2 = common.tmpfile(temporary_dir, '.tif')
     common.run(["plambda", disp, "x 0 join", "-o", tmp1])
     common.run(["backflow", tmp1, im2, tmp2])
     common.run(["plambda", disp, im1, tmp2, "x isfinite y isfinite z isfinite and and vmul", "-o", mask])
 
 
-def compute_disparity_map(im1, im2, disp, mask, algo, disp_min=None,
+def compute_disparity_map(im1, im2, disp, mask, algo, cfg, disp_min=None,
                           disp_max=None, timeout=600, max_disp_range=None,
                           extra_params=''):
     """
@@ -124,14 +123,14 @@ def compute_disparity_map(im1, im2, disp, mask, algo, disp_min=None,
 
         win = 3  # matched block size. It must be a positive odd number
         lr = 1  # maximum difference allowed in the left-right disparity check
-        cost = common.tmpfile('.tif')
+        cost = common.tmpfile(cfg['temporary_dir'], '.tif')
         common.run('sgbm {} {} {} {} {} {} {} {} {} {}'.format(im1, im2,
                                                                disp, cost,
                                                                disp_min,
                                                                disp_max,
                                                                win, p1, p2, lr))
 
-        create_rejection_mask(disp, im1, im2, mask)
+        create_rejection_mask(disp, im1, im2, mask, cfg['temporary_dir'])
 
     if algo == 'tvl1':
         tvl1 = 'callTVL1.sh'
@@ -185,14 +184,14 @@ def compute_disparity_map(im1, im2, disp, mask, algo, disp_min=None,
             timeout=timeout,
         )
 
-        create_rejection_mask(disp, im1, im2, mask)
+        create_rejection_mask(disp, im1, im2, mask, cfg['temporary_dir'])
 
 
     if algo == 'mgm_multi_lsd':
         ref = im1
         sec = im2
-        wref = common.tmpfile('.tif')
-        wsec = common.tmpfile('.tif')
+        wref = common.tmpfile(cfg['temporary_dir'], '.tif')
+        wsec = common.tmpfile(cfg['temporary_dir'], '.tif')
         # TODO TUNE LSD PARAMETERS TO HANDLE DIRECTLY 12 bits images?
         # image dependent weights based on lsd segments
         with rasterio.open(ref, "r") as f:
@@ -263,7 +262,7 @@ def compute_disparity_map(im1, im2, disp, mask, algo, disp_min=None,
             timeout=timeout,
         )
 
-        create_rejection_mask(disp, im1, im2, mask)
+        create_rejection_mask(disp, im1, im2, mask, cfg['temporary_dir'])
 
 
     if algo == 'mgm_multi':
@@ -307,7 +306,7 @@ def compute_disparity_map(im1, im2, disp, mask, algo, disp_min=None,
             timeout=timeout,
         )
 
-        create_rejection_mask(disp, im1, im2, mask)
+        create_rejection_mask(disp, im1, im2, mask, cfg['temporary_dir'])
 
     if (algo == 'micmac'):
         # add micmac binaries to the PATH environment variable

s2p/common.py

@@ -15,8 +15,6 @@
 import rasterio
 
 
-from s2p.config import cfg
-
 
 # silent rasterio NotGeoreferencedWarning
 warnings.filterwarnings("ignore",
@@ -38,18 +36,18 @@ def remove(target):
     except OSError:
         pass
 
-def garbage_cleanup():
+def garbage_cleanup(clean_tmp=True):
     """
     Removes all the files listed in the global variable 'garbage'.
     """
-    if cfg['clean_tmp']:
+    if clean_tmp:
         while garbage:
             remove(garbage.pop())
 
 
-def tmpfile(ext=''):
+def tmpfile(temporary_dir, ext=''):
     """
-    Creates a temporary file in the cfg['temporary_dir'] directory.
+    Creates a temporary file in the temporary_dir directory.
 
     Args:
         ext: desired file extension. The dot has to be included.
@@ -61,7 +59,7 @@ def tmpfile(ext=''):
     at the end of the pipeline.
     """
     fd, out = tempfile.mkstemp(suffix=ext, prefix='s2p_',
-                               dir=os.path.expandvars(cfg['temporary_dir']))
+                               dir=os.path.expandvars(temporary_dir))
     os.close(fd)           # http://www.logilab.org/blogentry/17873
     garbage.append(out)
     return out

s2p/fusion.py

@@ -9,7 +9,6 @@
 import numpy as np
 import rasterio
 
-from s2p.config import cfg
 from s2p import common
 
 
@@ -22,7 +21,7 @@ def average_if_close(x, threshold):
         return np.nanmedian(x)
 
 
-def merge_n(output, inputs, offsets, averaging='average_if_close', threshold=1):
+def merge_n(output, inputs, offsets, averaging='average_if_close', threshold=1, debug=False):
     """
     Merge n images of equal sizes by taking the median/mean/min/max pixelwise.
 
@@ -47,7 +46,7 @@ def merge_n(output, inputs, offsets, averaging='average_if_close', threshold=1):
     for i, img in enumerate(inputs):
         with rasterio.open(img, 'r') as f:
             x[:, :, i] = f.read(1) - offsets[i]
-        if cfg['debug']:
+        if debug:
             common.rasterio_write('{}_registered.tif'.format(os.path.splitext(img)[0]),
                                   x[:, :, i] + np.mean(offsets))
 

s2p/initialization.py

@@ -100,12 +100,10 @@ def check_parameters(d):
 
 def build_cfg(cfg, user_cfg):
     """
-    Populate a dictionary containing the s2p parameters from a user config file.
-
-    This dictionary is contained in the global variable 'cfg' of the config
-    module.
+    Populate a default cfg dictionary with the s2p parameters from a user config file.
 
     Args:
+        cfg: default config dictionary
         user_cfg: user config dictionary
     """
     # check that all the mandatory arguments are defined
@@ -312,7 +310,7 @@ def is_tile_all_nodata(path:str, window:rasterio.windows.Window):
             return False
 
 
-def is_this_tile_useful(x, y, w, h, images, images_sizes, border_margin):
+def is_this_tile_useful(x, y, w, h, images, images_sizes, border_margin, cfg):
     """
     Check if a tile contains valid pixels.
 
@@ -336,7 +334,7 @@ def is_this_tile_useful(x, y, w, h, images, images_sizes, border_margin):
 
     rpc = images[0]['rpcm']
     for img, size in zip(images[1:], images_sizes[1:]):
-        coords = rpc_utils.corresponding_roi(rpc, img['rpcm'], x, y, w, h)
+        coords = rpc_utils.corresponding_roi(rpc, img['rpcm'], x, y, w, h, cfg)
         if rectangles_intersect(coords, (0, 0, size[1], size[0])):
             break  # the tile is partly contained
     else:  # we've reached the end of the loop hence the tile is not contained
@@ -346,7 +344,7 @@ def is_this_tile_useful(x, y, w, h, images, images_sizes, border_margin):
     cld_msk = images[0]['cld']
     wat_msk = images[0]['wat']
     mask = masking.image_tile_mask(x, y, w, h, roi_msk, cld_msk, wat_msk,
-                                   images_sizes[0], border_margin=border_margin)
+                                   images_sizes[0], border_margin=border_margin, temporary_dir=cfg['temporary_dir'])
     if not mask.any():
         return False, None
     return True, mask
@@ -388,6 +386,7 @@ def tiles_full_info(cfg, tw, th, tiles_txt, create_masks=False):
                                                    cfg['images'],
                                                    images_sizes,
                                                    cfg['border_margin'],
+                                                   cfg,
                                                    tilewise=False,
                                                    timeout=cfg['timeout'],
                                                    )

s2p/masking.py

@@ -16,7 +16,7 @@
 
 
 def image_tile_mask(x, y, w, h, roi_gml=None, cld_gml=None, raster_mask=None,
-                    img_shape=None, border_margin=10):
+                    img_shape=None, border_margin=10, temporary_dir=None):
     """
     Compute a validity mask for an image tile from vector/raster image masks.
 
@@ -44,7 +44,7 @@ def image_tile_mask(x, y, w, h, roi_gml=None, cld_gml=None, raster_mask=None,
     mask = np.ones((h, w), dtype=bool)
 
     if roi_gml is not None:  # image domain mask (polygons)
-        tmp = common.tmpfile('.png')
+        tmp = common.tmpfile(temporary_dir, '.png')
         subprocess.check_call('cldmask %d %d -h "%s" %s %s' % (w, h, hij,
                                                                roi_gml, tmp),
                               shell=True)
@@ -55,7 +55,7 @@ def image_tile_mask(x, y, w, h, roi_gml=None, cld_gml=None, raster_mask=None,
             return mask
 
     if cld_gml is not None:  # cloud mask (polygons)
-        tmp = common.tmpfile('.png')
+        tmp = common.tmpfile(temporary_dir, '.png')
         subprocess.check_call('cldmask %d %d -h "%s" %s %s' % (w, h, hij,
                                                                cld_gml, tmp),
                               shell=True)

s2p/pointing_accuracy.py

@@ -10,7 +10,6 @@
 from s2p import sift
 from s2p import rpc_utils
 from s2p import estimation
-from s2p.config import cfg
 
 
 def error_vectors(m, F, ind='ref'):
@@ -60,7 +59,7 @@ def error_vectors(m, F, ind='ref'):
     return np.vstack((np.multiply(a, l[:, 0]), np.multiply(a, l[:, 1]))).T
 
 
-def local_translation(r1, r2, x, y, w, h, m):
+def local_translation(r1, r2, x, y, w, h, m, cfg):
     """
     Estimates the optimal translation to minimise the relative pointing error
     on a given tile.
@@ -80,7 +79,7 @@ def local_translation(r1, r2, x, y, w, h, m):
     """
     # estimate the affine fundamental matrix between the two views
     n = cfg['n_gcp_per_axis']
-    rpc_matches = rpc_utils.matches_from_rpc(r1, r2, x, y, w, h, n)
+    rpc_matches = rpc_utils.matches_from_rpc(r1, r2, x, y, w, h, n, cfg)
     F = estimation.affine_fundamental_matrix(rpc_matches)
 
     # compute the error vectors
@@ -101,7 +100,7 @@ def local_translation(r1, r2, x, y, w, h, m):
 
 def compute_correction(img1, img2, rpc1, rpc2, x, y, w, h,
                        method, sift_thresh, epipolar_threshold,
-                       matching_method, min_value, max_value, confidence_threshold):
+                       matching_method, min_value, max_value, confidence_threshold, cfg):
     """
     Computes pointing correction matrix for specific ROI
 
@@ -126,11 +125,11 @@ def compute_correction(img1, img2, rpc1, rpc2, x, y, w, h,
         raise ValueError(f"width or height <= 0 for:\n{img1}\n{img2}\nx={x}, y={y}, w={w}, h={h}. Try a different"
                          f"tilesize or different ROI.")
     m = sift.matches_on_rpc_roi(img1, img2, rpc1, rpc2, x, y, w, h,
-                                method, sift_thresh, epipolar_threshold,
+                                method, sift_thresh, epipolar_threshold, cfg,
                                 matching_method, min_value, max_value, confidence_threshold)
 
     if m is not None:
-        A = local_translation(rpc1, rpc2, x, y, w, h, m)
+        A = local_translation(rpc1, rpc2, x, y, w, h, m, cfg)
     else:
         A = None