def run(input_dir, phantom, gt_path,
mask_path=None,
dtypes=(np.float32, np.float16, np.uint8),
suffix=".raw",
output_dir="../data/simresults"
):
"""
Compute RMSE on a set of volumes in the given `input_dir`. Only files
ending with `suffix` are considered.
Specify `gt_path` and `mask_path` to create ground truth and mask arrays
prior to looping over files.
`dtypes` order: ground truth, experiment, mask
"""
import os
files = [f for f in os.listdir(input_dir) if f.endswith(suffix)]
import re
tv_grad_pattern = re.compile(".*-(\d+\.\d+)tv")
from utils import find_filtermode, find_recomode
results = []
ground_truth = np.fromfile(gt_path, dtype=dtypes[0])
mask = None if mask_path is None else np.fromfile(mask_path, dtype=dtypes[2])
for f in files:
rmse = compute_rmse_from_exp_path(
os.path.join(input_dir, f),
ground_truth,
mask,
dtype=dtypes[1]
)
filMode = find_filtermode(f)
frms = f[:3]
flux = f[8:13]
tvGrad = tv_grad_pattern.search(f).group(1)
recoMode = find_recomode(f)
results.append((
int(filMode),
int(frms),
int(flux),
float(tvGrad),
float(rmse),
int(recoMode),
# still hardcoded...
3
))
from constants import RMSE_FILE
rmse_filepath = os.path.join(output_dir, RMSE_FILE.format(phantom))
write_header = not os.path.exists(rmse_filepath)
with open(rmse_filepath, 'a+') as rf:
if write_header:
rf.write("#fmode,frms,flux,tvGrad,rmse,recoMode,numIter\n")
for result in results:
rf.write(
','.join([str(r) for r in result]) + '\n'
)
NOISELEVEL_OUTPUT_DIR = "../data/simresults"
NOISELEVEL_FILEPATH = os.path.join(
NOISELEVEL_OUTPUT_DIR,
NOISELEVEL_FILE.format(PHANTOM_NAME+"-tv")
)
RMSE_INPUT_DIR = PHANTOM_INPUT_DIR
RMSE_OUTPUT_DIR = "../data/simresults"
RMSE_GROUND_TRUTH_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_GROUND_TRUTH_FILE)
RMSE_MASK_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_MASK_FILE)
# Ground truth and mask data needs to be loaded only once.
RMSE_GROUND_TRUTH = np.fromfile(RMSE_GROUND_TRUTH_PATH, dtype=np.float32)
RMSE_MASK = np.fromfile(RMSE_MASK_PATH, dtype=np.uint8)
RMSE_FILEPATH = os.path.join(
RMSE_OUTPUT_DIR,
RMSE_FILE.format(PHANTOM_NAME+"-tv")
)
# For single test run.
"""
PARAMETERS = {
"CBSIMULATION": {
"FRAMES": (479,),
"FLUX": (5e7,),
"NOISE": (True, )
},
"FILTERING": {
"MODE": (0, )
},
"RECO": {
"MODE": ("MLEM", ),
NOISELEVEL_OUTPUT_DIR = "../data/simresults"
NOISELEVEL_FILEPATH = os.path.join(
NOISELEVEL_OUTPUT_DIR,
NOISELEVEL_FILE.format(PHANTOM_NAME+"-sirt")
)
RMSE_INPUT_DIR = PHANTOM_INPUT_DIR
RMSE_OUTPUT_DIR = "../data/simresults"
RMSE_GROUND_TRUTH_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_GROUND_TRUTH_FILE)
RMSE_MASK_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_MASK_FILE)
# Ground truth and mask data needs to be loaded only once.
RMSE_GROUND_TRUTH = np.fromfile(RMSE_GROUND_TRUTH_PATH, dtype=np.float32)
RMSE_MASK = np.fromfile(RMSE_MASK_PATH, dtype=np.uint8)
RMSE_FILEPATH = os.path.join(
RMSE_OUTPUT_DIR,
RMSE_FILE.format(PHANTOM_NAME+"-sirt")
)
# For single test run.
"""
PARAMETERS = {
"CBSIMULATION": {
"FRAMES": (479,),
"FLUX": (5e7,),
"NOISE": (True, )
},
"FILTERING": {
"MODE": (0, )
},
"RECO": {
"MODE": ("MLEM", ),
EDGESHARPNESS_FILEPATH = os.path.join(
EDGESHARPNESS_OUTPUT_DIR,
EDGESHARPNESS_FILE.format(PHANTOM_NAME + "-tv", EDGESHARPNESS_ROI_NAME, EDGESHARPNESS_PREFILTER_SIGMA),
)
NOISELEVEL_OUTPUT_DIR = "../data/simresults"
NOISELEVEL_FILEPATH = os.path.join(NOISELEVEL_OUTPUT_DIR, NOISELEVEL_FILE.format(PHANTOM_NAME + "-tv"))
RMSE_INPUT_DIR = PHANTOM_INPUT_DIR
RMSE_OUTPUT_DIR = "../data/simresults"
RMSE_GROUND_TRUTH_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_GROUND_TRUTH_FILE)
RMSE_MASK_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_MASK_FILE)
# Ground truth and mask data needs to be loaded only once.
RMSE_GROUND_TRUTH = np.fromfile(RMSE_GROUND_TRUTH_PATH, dtype=np.float32)
RMSE_MASK = np.fromfile(RMSE_MASK_PATH, dtype=np.uint8)
RMSE_FILEPATH = os.path.join(RMSE_OUTPUT_DIR, RMSE_FILE.format(PHANTOM_NAME + "-tv"))
# For single test run.
"""
PARAMETERS = {
"CBSIMULATION": {
"FRAMES": (479,),
"FLUX": (5e7,),
"NOISE": (True, )
},
"FILTERING": {
"MODE": (0, )
},
"RECO": {
"MODE": ("MLEM", ),
"RUNS": {
NOISELEVEL_OUTPUT_DIR = "../data/simresults"
NOISELEVEL_FILEPATH = os.path.join(
NOISELEVEL_OUTPUT_DIR,
NOISELEVEL_FILE.format(PHANTOM_NAME)
)
RMSE_INPUT_DIR = PHANTOM_INPUT_DIR
RMSE_OUTPUT_DIR = "../data/simresults"
RMSE_GROUND_TRUTH_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_GROUND_TRUTH_FILE)
RMSE_MASK_PATH = os.path.join(RMSE_INPUT_DIR, RMSE_MASK_FILE)
# Ground truth and mask data needs to be loaded only once.
RMSE_GROUND_TRUTH = np.fromfile(RMSE_GROUND_TRUTH_PATH, dtype=np.float32)
RMSE_MASK = np.fromfile(RMSE_MASK_PATH, dtype=np.uint8)
RMSE_FILEPATH = os.path.join(
RMSE_OUTPUT_DIR,
RMSE_FILE.format(PHANTOM_NAME)
)
# For single test run.
"""
PARAMETERS = {
"CBSIMULATION": {
"FRAMES": (479,),
"FLUX": (5e7,),
"NOISE": (True, )
},
"FILTERING": {
"MODE": (0, )
},
"RECO": {
"MODE": ("MLEM", ),