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removed PtychoEngine unnecessary methods

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swim
2026-07-30 20:56:58 +09:00
parent 02293389a1
commit 19f3cff188
3 changed files with 42 additions and 118 deletions
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ptycho/fold_slice.py
+38 -68
View File
@@ -2,6 +2,7 @@ import os
import sys
import shutil
import subprocess
import re
from typing import Any
from scipy.io import loadmat
import numpy as np
@@ -12,102 +13,71 @@ class FoldSlicePtychoEngine(PtychoEngine):
def __init__(self, config):
super().__init__(config)
self.fold_slice_output_dir = os.path.join(config['io']['result_dir'], 'fold_slice')
self._output_dir = os.path.join(config['io']['result_dir'], 'fold_slice')
self._fold_slice_path = self.config['ptycho']['path']
self._setup_txt_path = os.path.join(self._output_dir, 'setup.txt')
self._verbosity = self.config['io'].get('verbosity', 0)
def fold_slice_prepare(self) -> None:
config = self.config
fold_slice_output_dir = self.fold_slice_output_dir
def run(self, run_id="") -> None:
fold_slice_dict = {}
fold_slice_dict['raw_data'] = config['io']['input_data_path']
fold_slice_dict['result_dir'] = os.path.join(fold_slice_output_dir, '')
fold_slice_dict.update(config['ptycho']['params'])
fold_slice_dict['raw_data'] = self.config['io']['input_data_path']
fold_slice_dict['result_dir'] = os.path.join(self._output_dir, '')
fold_slice_dict.update(self.config['ptycho']['params'])
for key, value in fold_slice_dict.items():
if type(value) == bool:
fold_slice_dict[key] = str(value).lower()
if os.path.exists(os.path.join(fold_slice_output_dir)):
shutil.rmtree(os.path.join(fold_slice_output_dir))
os.makedirs(os.path.join(fold_slice_output_dir))
if os.path.exists(os.path.join(self._output_dir)):
shutil.rmtree(os.path.join(self._output_dir))
os.makedirs(os.path.join(self._output_dir))
with open(os.path.join(fold_slice_output_dir, 'setup.txt'), 'w') as f:
with open(os.path.join(self._output_dir, 'setup.txt'), 'w') as f:
f.write('\n\n')
for key, value in fold_slice_dict.items():
f.write(f"{key} {value}\n")
def run(self, header="") -> None:
self.fold_slice_prepare()
config = self.config
fold_slice_path = config['ptycho']['path']
setup_txt = os.path.join(self.fold_slice_output_dir, 'setup.txt')
verbosity = config['io'].get('verbosity', 0)
matlab_commands = [
f"cd('{fold_slice_path}');",
f"cd('{self._fold_slice_path}');",
"cd('ptycho');",
f"prepare_data('{setup_txt}');",
f"run_multislice_new('{setup_txt}');"
f"prepare_data('{self._setup_txt_path}');",
f"run_multislice_new('{self._setup_txt_path}');"
]
p = subprocess.Popen(
['matlab', '-batch', ' '.join(matlab_commands)],
stdout=subprocess.PIPE if verbosity > 0 else subprocess.DEVNULL,
stderr=subprocess.STDOUT if verbosity > 0 else subprocess.DEVNULL,
stdout=subprocess.PIPE if self._verbosity > 0 else subprocess.DEVNULL,
stderr=subprocess.STDOUT if self._verbosity > 0 else subprocess.DEVNULL,
text=True
)
if not verbosity == 0:
header = header + '[fold slice]'
if self._verbosity > 0:
for line in p.stdout: # type: ignore
sys.stdout.write(f'{header} {line}')
sys.stdout.write(f'[{run_id}] [fold_slice] {line}')
p.stdout.close() # type: ignore
else:
print(f"fold_slice running. Set verbosity > 0 for full fold_slice output.")
p.wait()
def get_output_mat_path(self) -> str:
config = self.config
fold_slice_output_dir = self.fold_slice_output_dir
roi_dir = os.path.join(
fold_slice_output_dir,
f"{config['ptycho']['params']['scan_number']}",
f"roi{config['ptycho']['params']['roi_label']}"
self._output_dir,
f"{self.config['ptycho']['params']['scan_number']}",
f"roi{self.config['ptycho']['params']['roi_label']}"
)
output_dir = os.path.join(roi_dir, next(os.walk(roi_dir))[1][0])
# image_path = os.path.join(output_dir, 'obj_phase_roi_sum', next(os.walk(os.path.join(output_dir, 'obj_phase_roi_sum')))[2][0])
output_mat_path = os.path.join(output_dir, f"Niter{config['ptycho']['params']['Niter']}.mat")
return output_mat_path
mat_path = os.path.join(output_dir, f"Niter{self.config['ptycho']['params']['Niter']}.mat")
image_path = os.path.join(output_dir, 'obj_phase_roi_sum', f"obj_phase_roi_sum_Niter{self.config['ptycho']['params']['Niter']}.tiff")
if not os.path.exists(mat_path):
raise FileNotFoundError(f"{mat_path} does not exist. Please check the fold_slice output.")
if not os.path.exists(image_path):
raise FileNotFoundError(f"{image_path} does not exist. Please check the fold_slice output.")
def output(self) -> Any:
if self._output is None:
output_mat_path = self.get_output_mat_path()
if not os.path.exists(output_mat_path):
raise FileNotFoundError(f"Result directory {output_mat_path} does not exist. Please check the fold_slice output.")
self._output = loadmat(output_mat_path)
return self._output
self._output = loadmat(mat_path)
self._metric = -np.log(float(self._output['outputs']['fourier_error_out'][0][0].squeeze()[-1]))
def recon_object(self) -> np.ndarray:
if self._recon_object is None:
output = self.output()
self._recon_object = output['object'] # type: ignore
return self._recon_object
def recon_probe(self) -> np.ndarray:
if self._recon_probe is None:
output = self.output()
self._recon_probe = output['probe'] # type: ignore
return self._recon_probe
def metric(self) -> float:
if self._metric is None:
output = self.output()
fourier_error = output['outputs']['fourier_error_out'][0][0].squeeze()
metric = float(fourier_error[-1])
self._metric = metric
return self._metric
os.makedirs(os.path.join(self.config['io']['result_dir'], "mat"), exist_ok=True)
os.makedirs(os.path.join(self.config['io']['result_dir'], "tiff"), exist_ok=True)
shutil.copy(mat_path, os.path.join(self.config['io']['result_dir'], "mat", f"{self._metric:.4f}_{run_id}.mat"))
shutil.copy(image_path, os.path.join(self.config['io']['result_dir'], "tiff", f"{self._metric:.4f}_{run_id}.tiff"))
ptycho/ptycho_base.py
+1 -21
View File
@@ -7,28 +7,8 @@ class PtychoEngine(ABC):
def __init__(self, config):
self.config = config
self._output = None
self._recon_object = None
self._recon_probe = None
self._metric = None
@abstractmethod
def run(self) -> None:
pass
@abstractmethod
def output(self) -> Any:
pass
@abstractmethod
def recon_object(self) -> Any:
pass
@abstractmethod
def recon_probe(self) -> Any:
pass
@abstractmethod
def metric(self) -> float:
def run(self, run_id="") -> None:
pass
ptycho/ptycho_example.py
+3 -29
View File
@@ -10,35 +10,9 @@ class ExamplePtychoEngine(PtychoEngine):
def __init__(self, config):
super().__init__(config)
self._metric = 0.0
# run single ptychography job based on `config`
def run(self) -> None:
print("[ExamplePtychoEngine] Sleeping for 0.1 second.")
def run(self, run_id="") -> None:
print(f"[{run_id}] [ExamplePtychoEngine] Sleeping for 0.1 second.")
time.sleep(0.1)
# save outputs to self._output
def output(self) -> Any:
if self._output is None:
pass
return self._output
# return reconstructed object (numpy array)
def recon_object(self) -> Any:
if self._recon_object is None:
output = self.output()
pass
return self._recon_object
# return reconstructed probe (numpy array)
def recon_probe(self) -> Any:
if self._recon_probe is None:
output = self.output()
pass
return self._recon_probe
# return metric value for Bayesian optimization
def metric(self) -> float:
if self._metric is None:
output = self.output()
self._metric = random.uniform(0, 1)
return self._metric