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Fix rectify map substrate size difference. Addresses issues in #134; …
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…removes need for FixNoDat
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@CameronBodine
CameronBodine committed Jan 1, 2025
1 parent e09acab commit d62863e
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Showing 2 changed files with 69 additions and 36 deletions.
34 changes: 24 additions & 10 deletions src/class_portstarObj.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1997,18 +1997,32 @@ def _mapSubstrate(self, map_class_method, chunk, npzs):


###############################################################
# Merge arrays (may need to add a size check, skipping for now)
# Left start ping, right end ping, top port, bottom star
portSub = np.rot90(portSub, k=2, axes=(1,0))
portSub = np.fliplr(portSub)
mergeSub = np.concatenate((portSub, starSub), axis=0)
# Merge arrays

del portSub, starSub
# Check to see if there is a size mismatch. If so, resize and rectify each individually
if portSub.shape[1] == starSub.shape[1]:
portSub = np.rot90(portSub, k=2, axes=(1,0))
portSub = np.fliplr(portSub)
mergeSub = np.concatenate((portSub, starSub), axis=0)

del portSub, starSub

# Do rectification
self._rectify(mergeSub, chunk, 'map_substrate')
# Do rectification
self._rectify(mergeSub, chunk, 'map_substrate')
del mergeSub

else:
# Rectify each individually
# Port
self.port.sonDat = portSub
self.port.rect_wcr = True
self.port._rectSonParallel(chunk, son=False)

# Star
self.star.sonDat = starSub
self.star.rect_wcr = True
self.star._rectSonParallel(chunk, son=False)

del mergeSub
gc.collect()

return
Expand Down Expand Up @@ -2756,4 +2770,4 @@ def __str__(self):
for item in temp:
output += '\n\t'
output += "{} : {}".format(item, temp[item])
return output
return output
71 changes: 45 additions & 26 deletions src/class_rectObj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from skimage.transform import warp
from rasterio.transform import from_origin
from rasterio.enums import Resampling
from PIL import Image
from PIL import Image, ImageColor
from shapely.geometry import Polygon

from matplotlib import colormaps
Expand Down Expand Up @@ -1444,8 +1444,11 @@ def _rectSonParallel(self,
self._pixresResize(gtiff)

if self.rect_wcr:
imgOutPrefix = 'rect_wcr'
outDir = os.path.join(self.outDir, imgOutPrefix) # Sub-directory
if son:
imgOutPrefix = 'rect_wcr'
outDir = os.path.join(self.outDir, imgOutPrefix) # Sub-directory
else:
imgOutPrefix = 'map_substrate_{}'.format(self.beamName)

if son:
try:
Expand Down Expand Up @@ -1482,51 +1485,73 @@ def _rectSonParallel(self,
# Warping substrate classification adds anomlies which must be removed
if not son:
# Set minSize
min_size = 1500
min_size = int((out.shape[0] + out.shape[1])/2)

# Set nan's to zero
out = np.nan_to_num(out, nan=0)#.astype('uint8')

# Label all regions
lbl = label(out)

# First set small objects to background value (0)
noSmall = remove_small_objects(lbl, min_size)
del lbl

# Punch holes in original label
holes = ~(noSmall==0)
del noSmall

l = out*holes
l = (out*holes).astype('uint8')

del holes, lbl

# Remove small holes
# Convert l to binary
binary_objects = l.astype(bool)
# Remove the holes
binary_filled = remove_small_holes(binary_objects, min_size)
binary_filled = remove_small_holes(binary_objects, min_size+100)
# Recover classification with holes filled
out = watershed(binary_filled, l, mask=binary_filled)
del binary_objects, binary_filled, l

out = out.astype('uint8')
del binary_filled, binary_objects, l

# Prepare colors
class_colormap = {0: '#3366CC',
1: '#DC3912',
2: '#FF9900',
3: '#109618',
4: '#990099',
5: '#0099C6',
6: '#DD4477',
7: '#66AA00',
8: '#B82E2E'}

for k, v in class_colormap.items():
rgb = ImageColor.getcolor(v, 'RGB')
class_colormap[k] = rgb

# Rotate 180 and flip
# https://stackoverflow.com/questions/47930428/how-to-rotate-an-array-by-%C2%B1-180-in-an-efficient-way
out = np.flip(np.flip(np.flip(out,1),0),1).astype('uint8')

projName = os.path.split(self.projDir)[-1] # Get project name
beamName = self.beamName # Determine which sonar beam we are working with
imgName = projName+'_'+imgOutPrefix+'_'+beamName+'_'+addZero+str(int(chunk))+'.tif' # Create output image name

if son:
projName = os.path.split(self.projDir)[-1] # Get project name
beamName = self.beamName # Determine which sonar beam we are working with
imgName = projName+'_'+imgOutPrefix+'_'+beamName+'_'+addZero+str(int(chunk))+'.tif' # Create output image name
gtiff = os.path.join(outDir, imgName) # Output file name
else:
outDir = os.path.join(self.substrateDir, 'map_sub')
if not os.path.exists(outDir):
os.mkdir(outDir)
gtiff = os.path.join(outDir, imgName) # Output file name
gtiff = gtiff.replace(imgOutPrefix, 'sub_map')
# Set output name
projName = os.path.split(self.projDir)[-1] # Get project name
imgName = projName+'_'+imgOutPrefix+'_'+addZero+str(int(chunk))+'.tif'
gtiff = os.path.join(self.outDir, imgName)

if pix_res != 0:
gtiff = gtiff.replace('.tif', 'temp.tif')

# Export georectified image
if son:
colormap = self.son_colorMap
else:
colormap = class_colormap
with rasterio.open(
gtiff,
'w',
Expand All @@ -1542,7 +1567,7 @@ def _rectSonParallel(self,
) as dst:
dst.nodata=0
dst.write(out,1)
dst.write_colormap(1, self.son_colorMap)
dst.write_colormap(1, colormap)
dst=None

del out, dst
Expand Down Expand Up @@ -1655,10 +1680,4 @@ def _getTiffAttributes(self, tif):

t = None

return bandCount, bandDtype, nodataVal






return bandCount, bandDtype, nodataVal

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