def run(input_dir, phantom, suffix=".raw", output_dir="../data/simresults"):
"""
Compute the variance in three ROIs of several volumes in the given input
directory. Pass a suffix if desired.
Run this in in scripts/ if no output_dir specified.
phantom | string, prefix to output filename
"""
from constants import NOISELEVEL_FILE
OUTPUT_FNAME = NOISELEVEL_FILE.format(phantom)
raw_files = [f for f in os.listdir(input_dir) if f.endswith(suffix)]
d = OrderedDict()
for f in tqdm(sorted(raw_files)):
img = np.fromfile(
os.path.join(input_dir, f),
dtype=np.float16).reshape((250, 512, 311))
variances = compute_var_from_volume(img)
# Fetch frame and flux info from filename.
filtermode = find_filtermode(f)
frms = f[:3]
flux = f[8:13]
d[f] = (filtermode, frms, flux) + variances
if d:
outpath = os.path.join(output_dir, OUTPUT_FNAME)
# output file will be sorted because first loop runs over sorted filenames.
write_header = not os.path.exists(outpath)
with open(outpath, 'a+') as f:
if write_header:
f.write("#fmode,fmrs,flux,var1,var2,var3\n")
for vtuple in d.values():
# CSV style
f.write("{},{},{},{},{},{}\n".format(*vtuple))
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'
)
def run(input_dir, phantom, roi_name, suffix=".raw",
output_dir="../data/simresults", **kwargs):
"""
Script to compute the ROI edge sharpness of several volumes in the given
input directory. Pass a suffix if desired.
Results are written to file. Manually specify parameters!
Run this in in scripts/ if no output_dir specified.
phantom | string, prefix to output filename
width | int, pixel width of region selected for ES computation, DEPRECATED
input_dir, output_dir | string
roi_name | name of ROI, taken from EDGESHARPNESS_ROIS
kwargs | passed to `compute_es_from_volume`: prefilter_sigma
passed to `compute_es_from_profile`: p0
"""
#input_dir = "/media/metzner/Z/Data/Head/forbild-phantoms/simresults/1noise"
raw_files = [f for f in os.listdir(input_dir) if f.endswith(suffix)]
prefilter_sigma = kwargs.get("prefilter_sigma", 0)
kwargs.pop("return_fig", None)
from constants import EDGESHARPNESS_FILE
output_fname = EDGESHARPNESS_FILE.format(
phantom,
roi_name,
prefilter_sigma
)
results = []
for fname in tqdm(sorted(raw_files)):
#fname = "479frms_5e+05flux_1noise_nofilter_fdk.raw"
volume = np.fromfile(os.path.join(input_dir, fname), dtype=np.float16).reshape((250,512,311))
edge_sharpness, edge_sharpness_delta = compute_es_from_volume(volume,
roi_name=roi_name, return_fig=False, **kwargs)
frms = fname[:3]
flux = fname[8:13]
filtermode = find_filtermode(fname)
results.append((filtermode, frms, flux, edge_sharpness, edge_sharpness_delta))
if results:
outpath = os.path.join(output_dir, output_fname)
write_header = not os.path.exists(outpath)
with open(outpath, 'a+') as f:
if write_header:
f.write("#fmode,frms,flux,shrpns,uncrty\n")
for result in results:
f.write(','.join([str(i) for i in result]) + '\n')