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grassloper
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- grassloper now uses improtools to debug image processing 

- the user can now change grassloper's parameters using command line arguments
This commit is contained in:
Guillaume Raffy 2022-11-30 18:30:17 +01:00
parent 3fa3a0afab
commit 0d41944c2a
2 changed files with 35 additions and 6 deletions
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10
README.md
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@ -18,5 +18,13 @@ bob@stykades:~/work/grassloper$ source ./grassloper.venv/bin/activate
# this automatically installs the packages that grassloper depends on # this automatically installs the packages that grassloper depends on
(grassloper.venv) bob@stykades:~/work/grassloper$ pip install -e ./grassloper.git (grassloper.venv) bob@stykades:~/work/grassloper$ pip install -e ./grassloper.git
# now that grassloper is installed in grassloper.venv and grassloper.venv is activated, simply run it using its command line 'grassloper' # now that grassloper is installed in grassloper.venv and grassloper.venv is activated, simply run it using its command line 'grassloper'
(grassloper.venv) bob@stykades:~/work/grassloper$ grassloper (grassloper.venv) bob@stykades:~/work/grassloper$ grassloper --help
```
# how to use
`grassloper`'s usage is described with the `--help` command line argument:
```sh
(grassloper.venv) bob@stykades:~/work/grassloper$ grassloper --help
``` ```

31
grassloper/main.py
View File

@ -6,6 +6,8 @@ import math
import h5py import h5py
import time import time
import scipy.stats import scipy.stats
import argparse
from improtools.imageprocessing import ImageProcessDebugger, IMovieProcessListener, NullMovieProcessListener, MovieProcessDebugger
def create_slope_image(image_width: int, image_height: int, p1_angle: float, p1_radius: float, bg_color: float = 0.0, fg_color: float = 1.0): def create_slope_image(image_width: int, image_height: int, p1_angle: float, p1_radius: float, bg_color: float = 0.0, fg_color: float = 1.0):
@ -91,8 +93,10 @@ class SlopeFinder():
def __init__(self, beads_radius: float): def __init__(self, beads_radius: float):
self.beads_radius = beads_radius self.beads_radius = beads_radius
def find_slope(self, trac_data: TracData, frame_index: int): def find_slope(self, trac_data: TracData, frame_index: int, mo_pro_listener: IMovieProcessListener = NullMovieProcessListener()):
isbead_image = SlopeFinder.create_isbead_image(trac_data, frame_index, self.beads_radius) isbead_image = SlopeFinder.create_isbead_image(trac_data, frame_index, self.beads_radius)
mo_pro_listener.onImage(isbead_image, 'isbead')
mo_pro_listener.onBaseImage(isbead_image, 'isbead')
cv2.imwrite('isbead_%04d.tif' % frame_index, isbead_image) cv2.imwrite('isbead_%04d.tif' % frame_index, isbead_image)
if False: if False:
kernel = np.ones((15, 15), np.uint8) kernel = np.ones((15, 15), np.uint8)
@ -138,6 +142,11 @@ class SlopeFinder():
y = [pt[1] for pt in surface_pts] y = [pt[1] for pt in surface_pts]
lin_regress_result = scipy.stats.linregress(x, y) lin_regress_result = scipy.stats.linregress(x, y)
print(lin_regress_result) print(lin_regress_result)
from_vertex = [0.0, lin_regress_result.intercept]
x_max = float(isbead_image.shape[1])
to_vertex = [x_max, lin_regress_result.intercept + x_max * lin_regress_result.slope]
mo_pro_listener.m_imageProcessListener.onLine( ((from_vertex[0], from_vertex[1]), (to_vertex[0], to_vertex[1])), 'slope')
@staticmethod @staticmethod
def create_isbead_image(trac_data: TracData, frame_index: int, particle_radius: float): def create_isbead_image(trac_data: TracData, frame_index: int, particle_radius: float):
@ -153,11 +162,23 @@ class SlopeFinder():
def main(): def main():
parser = argparse.ArgumentParser('grassloper', description='estimates the slope of granular surface', epilog='example: \n\tgrassloper --part-pos-file=./grassloper.git/samples/TracTrac/sample002_track.hdf5 --particle-radius=11.0 --debug-dir=\'./improdebug\'')
parser.add_argument('--part-pos-file', type=Path, default=None, required=True, help='the input file containing the particle positions')
parser.add_argument('--part-pos-file-format', type=str, choices=['tractrac-hdf5'], default='tractrac-hdf5', help='the file format of the input file that contains particle positions')
parser.add_argument('--particle-radius', type=float, required=True, help='the radius of the particles in pixels', default=11)
parser.add_argument('--debug-dir', type=Path, default=None, help='where to store image processing debug files')
args = parser.parse_args()
# python3 ./tractrac.git/Python/tractrac.py -f ./grassloper.git/samples/sample002.avi --output 1 -a --saveplot # python3 ./tractrac.git/Python/tractrac.py -f ./grassloper.git/samples/sample002.avi --output 1 -a --saveplot
trac_data = hdf5_to_trac_data('./grassloper.git/samples/TracTrac/sample002_track.hdf5') if args.debug_dir is not None:
slope_finder = SlopeFinder(beads_radius=11.0) mo_pro_listener = MovieProcessDebugger(args.debug_dir)
for frame_index in range(1, 2): else:
slope_finder.find_slope(trac_data, frame_index=frame_index) mo_pro_listener = NullMovieProcessListener()
trac_data = hdf5_to_trac_data(args.part_pos_file)
slope_finder = SlopeFinder(beads_radius=args.particle_radius)
for frame_index in range(1, 3):
mo_pro_listener.onImageProcessingStart()
slope_finder.find_slope(trac_data, frame_index=frame_index, mo_pro_listener=mo_pro_listener)
mo_pro_listener.onImageProcessingEnd()
# slope_image = create_slope_image(image_width=128, image_height=256, p1_angle=0.7, p1_radius=3.0) # slope_image = create_slope_image(image_width=128, image_height=256, p1_angle=0.7, p1_radius=3.0)
# cv2.imwrite(str(Path('toto.tif')), slope_image) # cv2.imwrite(str(Path('toto.tif')), slope_image)