shutil.copy(stimfile, copy_dir)
# get frame indices
frame_indices = []
with open(idx_txt, "r") as it:
for line in it:
frame_indices.append(int(line.strip()))
start_extr = frame_indices[0]
end_extr = frame_indices[-1]
# extract and convert v.t1 - v.t2 range
for idx in range(start_extr, (end_extr)):
# extract frame using RawReader
unconv_frame = rdr.get_frame(idx)
# trim junk pixels off of top
trimmed_frame = unconv_frame[junk:, :]
if args.flop:
trimmed_frame = np.fliplr(trimmed_frame)
# convert to fan shape
conv_frame = conv.convert(np.flipud(trimmed_frame))
ready_frame = np.flipud(conv_frame)
# create frame handle and save to copy dir
fh = basename + "." + "{0:05d}".format(idx) + ".bmp"
out_img = Image.fromarray(ready_frame)
out_img.save(os.path.join(copy_dir, fh))
print(header)
# visualize components on (approximately) converted fan, if desired
header.w = 127 # input image width
header.h = 1020 #255 # input image height
header.sf = 4000000 # for ultrasonix this is the vec-freq value
probe = Probe()
probe.radius = 10000 # based on '10' in transducer model number
probe.numElements = 128 # based on '128' in transducer model number
probe.pitch = 185 #205 # guess based on Ultrasonix C9-5/10 transducer
c = Converter(header, probe)
image_shape = (1020,127)#(255,127)
rdr = RawReader(rf, nscanlines=nscanlines, npoints = npoints)
print(rf)
for f in np.arange(0,(last_idx+1)):
d = rdr.get_frame(f).reshape(image_shape)
mag = np.max(d) - np.min(d)
d = (d-np.min(d))/mag*255
pcn = np.flipud(c.as_bmp(np.flipud(d)))
#pcn = c.as_bmp(d)
plt.title("Frame{:}, {:}".format((f+1),stim))
plt.imshow(pcn, cmap="Greys_r")
file_ending = "subj{:}-{:}-{:}.png".format(subject, stim,(f))
ultradir = os.path.join(os.path.basename(barename),file_ending)
savepath = os.path.join(expdir,ultradir)
print(savepath)
plt.savefig(savepath)
#
# consec_diffs = []
frameperc = int(last_idx * midperc)
print(frameperc)
frame_start = frameperc - prebuf
frame_end = frameperc + postbuf
print(frame_start)
print(frame_end)
consec_diffs = []
for f in np.arange(frame_start, frame_end):
# old method of getting frames
# minuend = get_frame(rf,f+1, myframesize, med_filter = True)
# subtrahend = get_frame(rf, f, myframesize, med_filter = True)
rdr = RawReader(
rf, nscanlines=nscanlines, npoints=npoints
) # or whatever the appropriate parameters actually are
minuend = rdr.get_frame(f + 1)
subtrahend = rdr.get_frame(f)
cdiff = minuend - subtrahend
cdiffnorm = np.linalg.norm(cdiff)
consec_diffs.append(cdiffnorm)
# print(consec_diffs)
mindiff, mindiff_idx = min(
(val, idx) for (idx, val) in enumerate(consec_diffs))
# print(mindiff)
# print(mindiff_idx)
rl_frame_idx = frame_start + mindiff_idx
print(rl_frame_idx)
# get frame, and check for NaN frames
change = 0
discard_acq = False
while True:
diff_list = []
diff2_list = []
for frame in sync_pm.tier('pulse_idx'):
diff = abs(frame.t1 - mid_timepoint)
diff_list.append(diff)
for frame in sync_pm.tier('raw_data_idx'):
diff2 = abs(frame.t1 - mid_timepoint)
diff2_list.append(diff2)
mid_pulse_idx_num = min(enumerate(diff_list), key=itemgetter(1))[0]
mid_raw_data_idx_num = min(enumerate(diff2_list), key=itemgetter(1))[0]
# get frame, and check for NaN frames
change = 0
discard_acq = False
while True:
pre_rawdata = rdr.get_frame(mid_pulse_idx_num)
if pre_rawdata is None:
mid_pulse_idx_num -= 1
mid_raw_data_idx_num -= 1 # TODO: necessary?
change += 1
if change > threshhold:
with open(logfile, "a") as log:
log.write(acq + "\t" + stim + "\t" + phone + "\t" +
"discarded" + "\t" + "passed threshhold")
print("Frame change threshhold passed; acq {} discarded".
format(acq))
discard_acq = True
break
else:
pass
else:
rlframes = []
for w in np.arange(0, len(prebufs)):
frame_start = frameperc - prebufs[w]
frame_end = frameperc + postbufs[w]
# print(frame_start)
# print(frame_end)
consec_diffs = []
for f in np.arange(frame_start, frame_end):
# old method of getting frames
# minuend = get_frame(rf,f+1, myframesize, med_filter = True)
# subtrahend = get_frame(rf, f, myframesize, med_filter = True)
rdr = RawReader(
rf, nscanlines=nscanlines, npoints=npoints
) # or whatever the appropriate parameters actually are
minuend = rdr.get_frame(f + 1)
# minuend = ndimage.median_filter(minuend, 3)
subtrahend = rdr.get_frame(f)
# subtrahend = ndimage.median_filter(subtrahend, 3)
cdiff = minuend - subtrahend
cdiffnorm = np.linalg.norm(cdiff)
consec_diffs.append(cdiffnorm)
# print(consec_diffs)
mindiff, mindiff_idx = min(
(val, idx) for (idx, val) in enumerate(consec_diffs))
# print(mindiff)
# print(mindiff_idx)
rl_frame_idx = frame_start + mindiff_idx
print(rl_frame_idx)
rlframes.append(rl_frame_idx)
diff2_list = []
for frame in sync_pm.tier('pulse_idx'):
diff = abs(frame.t1 - midpoint)
diff_list.append(diff)
for frame in sync_pm.tier('raw_data_idx'):
diff2 = abs(frame.t1 - midpoint)
diff2_list.append(diff2)
# TODO rewrite this chunk, temporary fix added
mid_pulse_idx_num = min(enumerate(diff_list),
key=itemgetter(1))[0]
mid_raw_data_idx_num = min(enumerate(diff2_list),
key=itemgetter(1))[0]
# get midpoint frame; discard if out of recorded range
try:
raw = rdr.get_frame(mid_pulse_idx_num - 1) # temporary fix
except IndexError: # thrown by RawReader.rdr if no frame at timepoint
# issue warning and move entire acq to discards folder
print("No frame available in {}, discarding".format(acq))
rdr.close()
if not os.path.isdir(disc):
os.mkdir(disc)
shutil.copytree(parent, os.path.join(disc, acq))
shutil.rmtree(parent)
continue
trim = raw[junk:, :]
# flop if needed
if args.flop:
trim = np.fliplr(trim)