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')
EXECUTABLE = os.path.join(BUILD_DIR, "bin/./ImFusionConsole")
PHANTOM_FILE = PHANTOMS[PHANTOM_NAME]["rawfile"]
PHANTOM_FILEPATH = os.path.join(PHANTOM_INPUT_DIR, PHANTOM_FILE)
IR_SCALING = PHANTOMS[PHANTOM_NAME]["ir_scaling"]
FDK_SCALING_FILE = "fdk_postscaling.dat"
FDK_SCALING_FILEPATH = os.path.join(VOLUME_OUTPUT_DIR, FDK_SCALING_FILE)
EDGESHARPNESS_INPUT_DIR = VOLUME_OUTPUT_DIR
EDGESHARPNESS_OUTPUT_DIR = "../data/simresults"
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.
def run(input_dir, phantom, save_volume,
suffix="_0filter_fdk.raw",
es_params=None,
compute_noise_level=False,
output_dir="../data/simresults",
**bf_kwargs
):
"""
Run postfilter routine on all files in input_dir that have the specified
suffix.
phantom | str, prefix for analysis files
save_volume | bool, whether to save the postfiltered volume or not
es_params | None or tuple(roi_name, sigma)
output_dir | Run this in scripts/ if not specified
bf_kwargs | sigmaISq, sigmaP, spacing, kernelScaling
"""
raw_nofilter_files = [f for f in listdir(input_dir) if f.endswith(suffix)]
COMPUTE_EDGESHARPNESS = es_params is not None
COMPUTE_ROI_VARIANCE = compute_noise_level
if COMPUTE_EDGESHARPNESS:
EDGESHARPNESS_FILEPATH = os.path.join(output_dir,
EDGESHARPNESS_FILE.format(phantom, *es_params))
ROI_VARIANCES_FILEPATH = os.path.join(output_dir, NOISELEVEL_FILE.format(phantom))
for i,file in tqdm(enumerate(raw_nofilter_files)):
# convert to float32 because pyopencl cannot handle float16.
img_in = np.fromfile(
os.path.join(input_dir, file),
dtype=np.float16).reshape((250,512,311)).astype(np.float32)
img_out = _apply_bilateral_filter(img_in, queue, **bf_kwargs)
# Analysis
if COMPUTE_ROI_VARIANCE:
variances = compute_var_from_volume(img_out)
write_header = not os.path.exists(ROI_VARIANCES_FILEPATH)
with open(ROI_VARIANCES_FILEPATH, 'a+') as rvf:
if write_header:
rvf.write("#fmode,fmrs,flux,var1,var2,var3\n")
rvf.write("{},{},{},{},{},{}\n".format(
2,
file[:3],
file[8:13],
*variances
)
)
if COMPUTE_EDGESHARPNESS:
es, esd = compute_es_from_volume(img_out, *es_params[::-1])
write_header = not os.path.exists(EDGESHARPNESS_FILEPATH)
with open(EDGESHARPNESS_FILEPATH, 'a+') as esf:
if write_header:
esf.write("#fmode,frms,flux,shrpns,uncrty\n")
esf.write("{},{},{},{},{}\n".format(
2, # post filtermode
file[:3],
file[8:13],
es,
esd
)
)
if save_volume:
# volume output directory is the input directory, i.e. on the server.
img_out.astype(np.float16).tofile(
os.path.join(
input_dir,
file.replace(suffix, "_2filter_fdk.raw")))