Testing alt.tbo with Atl3_bis 20171112a

import numpy as np
import matplotlib.pyplot as plt
import math
import os
import bim as USTk

for filename in os.listdir("./"):
    if filename.endswith(".DAT"):
        DATFile = os.path.join("", filename).split(".")[0]
        if not os.path.isfile(DATFile+".npz"):
            Arf = USTk.CreateUsPack(DATFile+".DAT")

NP1.DAT

OP1.DAT

NP3.DAT

NP4.DAT

NP2.DAT

OP3.DAT

## Creates the npz files from the DAT files, with reshaped signal, and filtered images
#  USTk.CreateUsPack(DATFile+".DAT") 
for filename in os.listdir("./"):
    if filename.endswith(".npz"):
        print filename
        DATFile = os.path.join("", filename).split(".")[0]   

        DATA = np.load(DATFile+".npz") 
        Image, rawSignal = DATA['arr_1'], DATA['arr_0']
        IMGs, GoodV, tmp = USTk.CreateRawImgs (Image,5)
        ## Cell 2
        plt.figure(figsize=(15,5))
        plt.imshow(np.transpose(tmp)) 
        for k in GoodV:
            plt.axvline(k, color='w', linestyle='--')
        plt.suptitle('Unpacking images in the '+DATFile+' file')
        plt.savefig('raw/Unpacking_'+DATFile+".jpg", bbox_inches='tight')
        plt.show()
        ## CEll 3
        N = len(IMGs)
        f, AX = plt.subplots(1, N, figsize=(15,5))
        for i in range(N):
            tmp = USTk.CreateSC(IMGs[i])
            AX[i].imshow(tmp[4])
        plt.suptitle('Getting a ultrasound image from a mechanical ATL3 ultrasound probe('+str(DATFile)+')')
        plt.savefig('Images_'+DATFile+".jpg", bbox_inches='tight')
        plt.show()

NP1.npz

NP2.npz

NP3.npz

NP4.npz

OP1.npz

/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py:1110: RuntimeWarning: Mean of empty slice.
  avg = a.mean(axis)
/usr/local/lib/python2.7/dist-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)

OP3.npz

DATFile = "NP2"
DATA = np.load(DATFile+".npz") 
Image, rawSignal = DATA['arr_1'], DATA['arr_0']
IMGs, GoodV, tmp = USTk.CreateRawImgsLR (Image,7,3)

## Cell 2
plt.figure(figsize=(15,5))
plt.imshow(np.transpose(tmp)) 
for k in GoodV:
    plt.axvline(k, color='w', linestyle='--')
plt.suptitle('Unpacking images in the '+DATFile+' file')
plt.savefig('Unpacking_'+DATFile+".jpg", bbox_inches='tight')
plt.show()

## CEll 3
N = len(IMGs)
f, AX = plt.subplots(1, N, figsize=(15,5))
for i in range(N):
    tmp = USTk.CreateSC(IMGs[i])
    AX[i].imshow(tmp[4])
plt.suptitle('Getting a ultrasound image from a mechanical ATL3 ultrasound probe('+str(DATFile)+')')
plt.savefig('ImagesIn_'+DATFile+".jpg", bbox_inches='tight')
plt.show()

Res = USTk.CreateSC(IMGs[0])[4]
for i in range(N-1):
    tmp = USTk.CreateSC(IMGs[i+1])[4]
    Res += tmp

plt.figure(figsize=(15,5))
plt.imshow(np.asarray(np.sqrt(Res)))
plt.show()

/usr/local/lib/python2.7/dist-packages/ipykernel/__main__.py:2: RuntimeWarning: invalid value encountered in sqrt
  from ipykernel import kernelapp as app

len(Res)

len(Res)

486

for k in range(len(Res)):
    for i in range(len(Res)):
        if Res[i][k] == 0:
            Res[i][k] = Res[20][243]

plt.figure(figsize=(15,5))
plt.imshow(np.asarray(np.sqrt(Res)))
plt.show()

/usr/local/lib/python2.7/dist-packages/ipykernel/__main__.py:2: RuntimeWarning: invalid value encountered in sqrt
  from ipykernel import kernelapp as app