Tutorial inhomogenous cylinder¶

import¶

In [7]:

import os
import sys
import numpy as np

root_folder = os.path.dirname(os.getcwd())
sys.path.insert(0, root_folder)
from cgc.geometry_correction import GeometryCorrection
import glob

import matplotlib.pyplot as plt
%matplotlib notebook

from ipywidgets import widgets, interact

initialize object¶

In [8]:

list_tiff = glob.glob('data/tiff/inhomogeneous*.tif')

o_cgc = GeometryCorrection(list_files=list_tiff)
o_cgc.load_files(notebook=True)

Display Images¶

In [9]:

list_images = o_cgc.list_data

fig1, (ax1, ax2) = plt.subplots(1, 2)

def plot(index):

    ax1.clear()
    ax1.imshow(list_images[index])

    ax2.clear()
    ax2.plot(list_images[index][0,:])

interact(plot,
        index = widgets.IntSlider(value=0,
                                max=len(list_images)-1),
                                continuous_update=False)

Out[9]:

<function __main__.plot>

define parameters¶

In [10]:

# center of cylinder
pixel_center = 256

# radius of cylinder
outer_radius = 200
inner_radius= 150

# define the parameters
o_cgc.define_parameters(inner_radius=inner_radius,
                        outer_radius=outer_radius,
                        pixel_center=pixel_center)

Run correction¶

In [11]:

o_cgc.correct(notebook=True)

Display data corrected¶

In [12]:

list_images_corrected = o_cgc.list_data_corrected

fig2, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(8,3))

def plot(index):

    ax1.clear()
    ax1.imshow(list_images_corrected[index])

    ax2.clear()
    max_y_value = np.nanmax(list_images_corrected[index][0, 1:])
    ax2.plot(list_images_corrected[index][0,:])
    ax2.set_ylim(0,max_y_value+1)

    ax3.clear()
    ax3.plot(list_images_corrected[index][0,:])

    plt.tight_layout()

interact(plot,
        index = widgets.IntSlider(value=0,
                                max=len(list_images_corrected)-1),
                                continuous_update=False)

Out[12]:

<function __main__.plot>