class Runner:
def __init__(self, scan_dir, work_dir):
self.recog = Recog.recog16()
self.store = Store()
self.plot = Plot()
self.work_dir = work_dir
self.scanner = Scanner(scan_dir, work_dir)
self.main_process()
def process(self, imgpath, amount):
place_id = ''.join(self.recog.recog(imgpath, box_view=True))
print(place_id)
parts_id = self.store.store(place_id, amount)
self.plot.plotAt(parts_id)
self.plot.plot()
def get_imgpath(self, imgpath):
return ''.join([self.work_dir, "/", imgpath])
def main_process(self):
while True:
if self.scanner.have_imgname:
imgname = self.scanner.get_imgname()
print("new image load: ", imgname)
self.process(self.get_imgpath(imgname), 1)
sleep(1)
def __init__(self, scan_dir, work_dir):
self.recog = Recog.recog16()
self.store = Store()
self.plot = Plot()
self.work_dir = work_dir
self.scanner = Scanner(scan_dir, work_dir)
self.main_process()
def plot_binned_energies_against_cp_phi_and_cp_theta(self):
(
cp_phi_values,
cp_theta_values,
free_energy_values,
count_values,
) = self.sort_cp_phi_cp_theta_binned_energies_for_contour()
scatter_params = {
"x_label": r"$\phi$",
"y_label": r"$\theta$",
"countour_levels": range(0, 6, 1),
}
plot_file_path = "custom_scripts/output/cp_phi_theta_free_energy_contour.png"
Plot().contour_plot(
cp_phi_values,
cp_theta_values,
free_energy_values,
plot_file_path,
scatter_params=scatter_params,
)
scatter_params = {
"x_label": r"$\phi$",
"y_label": r"$\theta$",
"x_major_tick": 60,
"x_end": 360,
"x_start": 0,
"y_end": 180,
"y_start": 0,
}
cp_phi_1d_values = [
cp_params["cp_phi"]
for cp_params in self.cp_trajectory_pucker_params.values()
]
cp_theta_1d_values = [
cp_params["cp_theta"]
for cp_params in self.cp_trajectory_pucker_params.values()
]
Plot().two_dimensional_scatter(
cp_phi_1d_values,
cp_theta_1d_values,
"custom_scripts/output/cp_phi_theta_scatter.png",
scatter_params=scatter_params,
)
def test_hist_unique(self):
"""Test hist_unique
Args:
self: TestPlot
Returns:
None
Raises:
None
"""
Plot.hist_unique([1, 2, 3, 4, 5, 1, 2], 'numbers', 'count',
'numbers-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
if not os.path.exists(self.TEST_PLOT_FILE_PATH):
self.assertTrue(False, 'Plot file not found')
# Invalid data_list
with self.assertRaises(PreconditionException) as context:
Plot.hist_unique(None, 'numbers', 'count', 'numbers-count',
self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid data_list' in str(context.exception))
# Invalid x_label
with self.assertRaises(PreconditionException) as context:
Plot.hist_unique([1, 2, 3, 4, 5, 1, 2], None, 'count',
'numbers-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid x_label' in str(context.exception))
# Invalid y_label
with self.assertRaises(PreconditionException) as context:
Plot.hist_unique([1, 2, 3, 4, 5, 1, 2], 'numbers', None,
'numbers-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid y_label' in str(context.exception))
# Invalid title
with self.assertRaises(PreconditionException) as context:
Plot.hist_unique([1, 2, 3, 4, 5, 1, 2], 'numbers', 'count', None,
self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid title' in str(context.exception))
def plot_free_energy_against_cp_theta(self):
free_energies = [
bin_value["free_energy_diff"]
for bin_value in self.cp_theta_bin_values.values()
]
scatter_params = {
"y_label": "delta G (kcal/mol)",
"x_label": "CP theta (deg)",
"y_start": 0,
"y_end": 8,
"x_major_tick": 30,
"x_end": 180,
"color": "black",
}
plot_file_path = "custom_scripts/output/free_energy_against_cp_theta.png"
Plot().two_dimensional_scatter(
self.cp_theta_bin_values.keys(),
free_energies,
plot_file_path,
scatter_params=scatter_params,
)
def plot_energy_with_average(self):
scatter_params = {
"y_label": "PE (kcal/mol)",
"x_label": "time (ns)",
"y_start": 230,
"y_end": 310,
"x_major_tick": 200,
"x_end": 2000,
"color": "black",
}
plot_file_path = "custom_scripts/output/trajectory_single_point_potential_energy_with_average.png"
# time_series = np.arange(0, 1500, 1500 / 60000)
time_series = np.arange(0, 2000, 2000 / 80000)
Plot().two_dimensional_scatter_plot_with_average(
time_series,
self.trajectory_pe_values,
np.arange(12.5, 2000, 25),
self.pe_periodic_mean_values,
plot_file_path,
scatter_params=scatter_params,
)
def _get_phase(self, phase_key, phase_dict):
if "generator" == phase_key:
return Generator.get_instance(self, self._base_dir,
self._global_dict, phase_dict,
self._failfast)
elif "solver" == phase_key:
return Solver.get_instance(self, self._base_dir, self._global_dict,
phase_dict, self._failfast)
elif "model" == phase_key:
return Model.get_instance(self, self._base_dir, self._global_dict,
phase_dict, self._failfast)
elif "leapfrog" == phase_key:
return Leapfrog.get_instance(self, self._base_dir,
self._global_dict, phase_dict,
self._failfast)
elif "plotter" == phase_key:
return Plot.get_instance(self, self._base_dir, self._global_dict,
phase_dict, self._failfast)
else:
assert False
return None
def plot_energy_against_cp_theta(
self, cp_trajectory_pucker_params, trajectory_energy_per_frame
):
trajectory_cp_theta = [
cp_params["cp_theta"] for cp_params in cp_trajectory_pucker_params.values()
]
scatter_params = {
"y_label": "PE (kcal/mol)",
"x_label": "CP theta (deg)",
"y_start": 260,
"y_end": 350,
"x_major_tick": 30,
"x_end": 180,
"color": "black",
}
plot_file_path = "custom_scripts/output/pe_against_cp_theta.png"
Plot().two_dimensional_scatter(
trajectory_cp_theta,
trajectory_energy_per_frame,
plot_file_path,
scatter_params=scatter_params,
)
def test_plot(self):
shelf = np.array(pd.read_csv("datasets/shelf.csv", header=None))
samples = np.random.randint(0,shelf.shape[0],20)
# print(samples)
plot = Plot()
for sample in samples:
plot.plotAt(sample)
plot.plot()
self.assertTrue(True)
def plot_energy_with_average(self):
scatter_params = {
"y_label": "rmsd (A)",
"x_label": "time (ns)",
"y_start": 0,
"y_end": 3,
"x_major_tick": 200,
"x_end": 1500,
"color": "black",
}
plot_file_path = "/home/timol/C6W/Studies/structure_analysis/output/aLRha13bDGlcNAc_3_10-aDGlc14bDGlcNAc_-31_-45_attempt_2/rmsd/rmsd.png"
time_series = np.arange(0, 1500, 1500 / 60000)
Plot().two_dimensional_scatter_plot_with_average(
time_series,
self.trajectory_pe_values,
np.arange(12.5, 1500, 25),
self.pe_periodic_mean_values,
plot_file_path,
scatter_params=scatter_params,
)
def test_bar(self):
"""Test bar
Args:
self: TestPlot
Returns:
None
Raises:
None
"""
Plot.bar(['a', 'e', 'i', 'o', 'u'], [1, 2, 3, 4, 5], 'vowels',
'counts', 'vowels-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
if not os.path.exists(self.TEST_PLOT_FILE_PATH):
self.assertTrue(False, 'Plot file not found')
# Invalid data_list1
with self.assertRaises(PreconditionException) as context:
Plot.bar(None, [1, 2, 3, 4, 5], 'alphabets', 'counts',
'alphabets-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid data_list1' in str(context.exception))
# Invalid data_list2
with self.assertRaises(PreconditionException) as context:
Plot.bar(['a', 'e', 'i', 'o', 'u'], None, 'alphabets', 'counts',
'alphabets-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid data_list2' in str(context.exception))
# Invalid x_label
with self.assertRaises(PreconditionException) as context:
Plot.bar(['a', 'e', 'i', 'o', 'u'], [1, 2, 3, 4, 5], None,
'counts', 'alphabets-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid x_label' in str(context.exception))
# Invalid y_label
with self.assertRaises(PreconditionException) as context:
Plot.bar(['a', 'e', 'i', 'o', 'u'], [1, 2, 3, 4, 5], 'alphabets',
None, 'alphabets-count', self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid y_label' in str(context.exception))
# Invalid title
with self.assertRaises(PreconditionException) as context:
Plot.bar(['a', 'e', 'i', 'o', 'u'], [1, 2, 3, 4, 5], 'alphabets',
'counts', None, self.TEST_PLOT_FILE_PATH,
self.TEST_SHOULD_SHOW_PLOT)
self.assertTrue('Invalid title' in str(context.exception))
def plot(self):
Plot.plot(self.asset_array, 'name')