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_pyhum_read bed picking changes #74

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_pyhum_read bed picking changes #74

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fb2190d
KDTree requires ndarray, not list
iannesbitt Mar 19, 2021
b2c8bc5
bed picking usability changes
iannesbitt Mar 19, 2021
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32 changes: 24 additions & 8 deletions PyHum/_pyhum_read.py
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Original file line number Diff line number Diff line change
Expand Up @@ -682,6 +682,7 @@ def read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, mo
if 2>1:
if bedpick == 1: # auto

print('Auto bed picking...')
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)

if len(dist_m)<len(bed):
Expand All @@ -700,6 +701,7 @@ def read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, mo

elif bedpick>1: # user prompt

print('Auto bed picking...')
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)

if len(dist_m)<len(bed):
Expand All @@ -712,25 +714,29 @@ def read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, mo
# manually intervene
fig = plt.figure()
ax = plt.gca()
print('Setting up bed picking figure...')
if chunkmode !=4:
im = ax.imshow(np.hstack(port_fp), cmap = 'gray', origin = 'upper')
else:
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
plt.plot(bed,'r')
plt.axis('normal'); plt.axis('tight')

pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
raw_input("Bed picking - are you ready? Press Enter to continue...")
print('Use the left mouse button to pick, right to delete, and center to end picking.')

pts1 = plt.ginput(n=300, timeout=-1) # it will wait for 300 clicks or the window to close (center mouse button)
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
plt.close()
del fig

if x1 != []: # if x1 is not empty
tree = KDTree(zip(np.arange(1,len(bed)), bed))
tree = KDTree(np.asarray(zip(np.arange(1,len(bed)), bed)))
try:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5, n_jobs=-1)
dist, inds = tree.query(np.asarray(zip(x1, y1)), k = 100, eps=5, n_jobs=-1)
except:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5)
dist, inds = tree.query(np.asarray(zip(x1, y1)), k = 100, eps=5)

b = np.interp(inds,x1,y1)
bed2 = bed.copy()
Expand All @@ -750,27 +756,37 @@ def read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, mo

if chunkmode!=4:
for k in range(len(port_fp)):
raw_input("Bed picking "+str(k+1)+" of "+str(len(port_fp))+", are you ready? 30 seconds. Press Enter to continue...")

bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp[k], cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds

raw_input("Bed picking "+str(k+1)+" of "+str(len(port_fp))+", are you ready? Press Enter to continue...")
print('Use the left mouse button to pick, right to delete, and center to end picking.')

pts1 = plt.ginput(n=300, timeout=-1) # it will wait for 300 clicks or the window to close (center mouse button)
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
plt.close()
del fig
beds.append(bed)
extent = np.shape(port_fp[k])[0]

bed = np.asarray(np.hstack(beds),'float')

else:
raw_input("Bed picking - are you ready? 30 seconds. Press Enter to continue...")

bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds

raw_input("Bed picking - are you ready? Press Enter to continue...")
print('Use the left mouse button to pick, right to delete, and center to end picking.')

pts1 = plt.ginput(n=300, timeout=-1) # it will wait for 300 clicks or the window to close (center mouse button)
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
Expand Down