niipre.py

#!/usr/bin/env python3

# Quick display of a Nifti image

# Packages
import nibabel as nb
import numpy as np
import os
import sys
from pathlib import Path
import matplotlib.pyplot as plt

# Disable Toolbar for plots
plt.rcParams['toolbar'] = 'None'

# Environment and file names
home = str(Path.home())
iFile = sys.argv[1]
oFile=(str(os.path.basename(iFile).replace('.nii.gz','.png').replace('.nii','.png')))

# Set rounding
np.set_printoptions(formatter={'float': lambda x: "{0:0.2f}".format(x)})



### IMPORT DATA ###
# Load data
image=nb.load(iFile)

# 3D data
if image.header['dim'][0]==3:
    data=image.get_data()
    # 4D data
elif  image.header['dim'][0]==4:
    data=image.get_data()[:,:,:,0]

# Header
header=image.header
    
# Set NAN to 0
data[np.isnan(data)] = 0



### PREPARE SOME PARAMETERS ###

# Spacing for Aspect Ratio
sX=header['pixdim'][1]
sY=header['pixdim'][2]
sZ=header['pixdim'][3]

# Size per slice
lX = data.shape[0]
lY = data.shape[1]
lZ = data.shape[2]

# Middle slice number
mX = int(lX/2)
mY = int(lY/2)
mZ = int(lZ/2)

# True middle point
tmX = lX/2.0
tmY = lY/2.0
tmZ = lZ/2.0



### ORIENTATION ###
qfX = image.get_qform()[0,0]
sfX = image.get_sform()[0,0]

if qfX < 0 and (sfX == 0 or sfX < 0):
    oL = 'R'
    oR = 'L'
elif qfX > 0 and (sfX == 0 or sfX > 0):
    oL = 'L'
    oR = 'R'
if sfX < 0 and (qfX == 0 or qfX < 0):
    oL = 'R'
    oR = 'L'
elif sfX > 0 and (qfX == 0 or qfX > 0):
    oL = 'L'
    oR = 'R'



### PLOTTING ###

# Plot main window
fig = plt.figure(
    facecolor='black',
    figsize=(5,4),
    dpi=200
)

# Black background
plt.style.use('dark_background')

# Set title
fig.canvas.set_window_title(oFile.replace('.png',''))


# Coronal
ax1=fig.add_subplot(2,2,1)
imgplot = plt.imshow(
    np.rot90(data[:,mY,:]),
    aspect=sZ/sX,
)
imgplot.set_cmap('gray')

ax1.hlines(tmZ, 0, lX, colors='red', linestyles='dotted', linewidth=.5)
ax1.vlines(tmX, 0, lZ, colors='red', linestyles='dotted', linewidth=.5)

plt.axis('off')


# Sagittal
ax2=fig.add_subplot(2,2,2)
imgplot = plt.imshow(
    np.rot90(data[mX,:,:]),
    aspect=sZ/sY,
)
imgplot.set_cmap('gray')

ax2.hlines(tmZ, 0, lY, colors='red', linestyles='dotted', linewidth=.5)
ax2.vlines(tmY, 0, lZ, colors='red', linestyles='dotted', linewidth=.5)

plt.axis('off')


# Axial
ax3=fig.add_subplot(2,2,3)
imgplot = plt.imshow(
    np.rot90(data[:,:,mZ]),
    aspect=sY/sX
)
imgplot.set_cmap('gray')

ax3.hlines(tmY, 0, lX, colors='red', linestyles='dotted', linewidth=.5)
ax3.vlines(tmX, 0, lY, colors='red', linestyles='dotted', linewidth=.5)

plt.axis('off')

plt.text(-10, mY+5, oL, fontsize=9, color='red') # Label on left side


# Textual information
# sform code
sform=np.round(image.get_sform(),decimals=2)
sform_txt=str(sform).replace('[',' ').replace(']',' ').replace(' ','   ').replace('   -','  -')

# qform code
qform=np.round(image.get_qform(),decimals=2)
qform_txt=str(qform).replace('[',' ').replace(']',' ').replace(' ','   ').replace('   -','  -')

# Dimensions
dims=str(data.shape).replace(', ',' x ').replace('(','').replace(')','')
dim=("Dimensions: "+dims)

# Spacing
spacing=("Spacing: "
         +str(np.round(sX, decimals=2))
         +" x "
         +str(np.round(sY, decimals=2))
         +" x "
         +str(np.round(sZ, decimals=2))
         +" mm"
)

# Data type
type=image.header.get_data_dtype()
type_str=("Data type: "+str(type))

# Volumes
volumes=("Volumes: "+str(image.header['dim'][4]))

# Range
min=np.round(np.amin(data), decimals=2)
max=np.round(np.amax(data), decimals=2)
range=("Range: "+str(min)+" - "+str(max))

text=(
    dim+"\n"
    +spacing+"\n"
    +volumes+"\n"
    +type_str+"\n"
    +range+"\n\n"
    +"sform code:\n"
    +sform_txt+"\n"
    +"\nqform code:\n"
    +qform_txt
)

# Plot text subplot
ax4=fig.add_subplot(2,2,4)
plt.text(
    0.15,
    0.95,
    text,
    horizontalalignment='left',
    verticalalignment='top',
    size=6,
    color='white',
)
plt.axis('off')

# Adjust whitespace
plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)

# Display
plt.show()