moved plotting utilities from demos (#424)

* moved plotting utilities from demos

* added plt.show()

* add utilities package

* removed print statement

* added numpy import

6 files changed, 516 insertions, 1 deletions

diff --git a/Wrappers/Python/ccpi/framework/TestData.py b/Wrappers/Python/ccpi/framework/TestData.py
index 2bb18ce..c035850 100755
--- a/Wrappers/Python/ccpi/framework/TestData.py
+++ b/Wrappers/Python/ccpi/framework/TestData.py
@@ -86,7 +86,6 @@ class TestData(object):
             
         else:
             tmp = Image.open(os.path.join(self.data_dir, which))
-            print (tmp)
             bands = tmp.getbands()
             if len(bands) > 1:
                 ig = ImageGeometry(voxel_num_x=size[0], voxel_num_y=size[1], channels=len(bands), 
diff --git a/Wrappers/Python/ccpi/utilities/__init__.py b/Wrappers/Python/ccpi/utilities/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/Wrappers/Python/ccpi/utilities/__init__.py
diff --git a/Wrappers/Python/ccpi/utilities/display.py b/Wrappers/Python/ccpi/utilities/display.py
new file mode 100644
index 0000000..cfb20dc
--- /dev/null
+++ b/Wrappers/Python/ccpi/utilities/display.py
@@ -0,0 +1,317 @@
+# -*- coding: utf-8 -*-
+# Copyright 2019 Science Technology Facilities Council
+# Copyright 2019 University of Manchester
+#
+# This work is part of the Core Imaging Library developed by Science Technology
+# Facilities Council and University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import print_function, division
+import matplotlib.pyplot as plt
+from matplotlib import gridspec
+import numpy
+from ccpi.framework import ImageGeometry
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+
+def plotter2D(datacontainers, titles=None, fix_range=False, stretch_y=False, cmap='gray', axis_labels=None):
+    '''plotter2D(datacontainers=[], titles=[], fix_range=False, stretch_y=False, cmap='gray', axes_labels=['X','Y'])
+    
+    plots 1 or more 2D plots in an (n x 2) matix
+    multiple datasets can be passed as a list
+    
+    Can take ImageData, AquistionData or numpy.ndarray as input
+    '''
+    if(isinstance(datacontainers, list)) is False:
+        datacontainers = [datacontainers]
+
+    if titles is not None:
+        if(isinstance(titles, list)) is False:
+            titles = [titles]
+            
+
+    
+    nplots = len(datacontainers)
+    rows = int(round((nplots+0.5)/2.0))
+
+    fig, (ax) = plt.subplots(rows, 2,figsize=(15,15))
+
+    axes = ax.flatten() 
+
+    range_min = float("inf")
+    range_max = 0
+    
+    if fix_range == True:
+        for i in range(nplots):
+            if type(datacontainers[i]) is numpy.ndarray:
+                dc = datacontainers[i]
+            else:
+                dc = datacontainers[i].as_array()
+                
+            range_min = min(range_min, numpy.amin(dc))
+            range_max = max(range_max, numpy.amax(dc))
+        
+    for i in range(rows*2):
+        axes[i].set_visible(False)
+
+    for i in range(nplots):
+        axes[i].set_visible(True)
+        
+        if titles is not None:
+            axes[i].set_title(titles[i])
+       
+        if axis_labels is not None:
+            axes[i].set_ylabel(axis_labels[1])
+            axes[i].set_xlabel(axis_labels[0]) 
+            
+        if type(datacontainers[i]) is numpy.ndarray:
+            dc = datacontainers[i]          
+        else:
+            dc = datacontainers[i].as_array()
+            
+            if axis_labels is None:
+                axes[i].set_ylabel(datacontainers[i].dimension_labels[0])
+                axes[i].set_xlabel(datacontainers[i].dimension_labels[1])        
+        
+        
+        sp = axes[i].imshow(dc, cmap=cmap, origin='upper', extent=(0,dc.shape[1],dc.shape[0],0))
+    
+        
+        im_ratio = dc.shape[0]/dc.shape[1]
+        
+        if stretch_y ==True:   
+            axes[i].set_aspect(1/im_ratio)
+            im_ratio = 1
+            
+        plt.colorbar(sp, ax=axes[i],fraction=0.0467*im_ratio, pad=0.02)
+        
+        if fix_range == True:
+            sp.set_clim(range_min,range_max)
+    plt.show()
+
+
+def channel_to_energy(channel):
+    # Convert from channel number to energy using calibration linear fit
+    m = 0.2786
+    c = 0.8575
+    # Add on the offset due to using a restricted number of channel (varies based on user choice)
+    shifted_channel = channel + 100
+    energy = (shifted_channel * m) + c
+    energy = format(energy,".3f")
+    return energy
+
+
+def show2D(x, title='', **kwargs):
+    
+    cmap = kwargs.get('cmap', 'gray')
+    font_size = kwargs.get('font_size', [12, 12])
+    minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max())))
+    
+    # get numpy array
+    tmp = x.as_array()
+      
+    # labels for x, y      
+    labels = kwargs.get('labels', ['x','y']) 
+    
+    
+    # defautl figure_size
+    figure_size = kwargs.get('figure_size', (10,5)) 
+    
+    # show 2D via plt
+    fig, ax = plt.subplots(figsize = figure_size)  
+    im = ax.imshow(tmp, cmap = cmap, vmin=min(minmax), vmax=max(minmax))
+    ax.set_title(title, fontsize = font_size[0])
+    ax.set_xlabel(labels[0], fontsize = font_size[1])
+    ax.set_ylabel(labels[1], fontsize = font_size[1]) 
+    divider = make_axes_locatable(ax) 
+    cax1 = divider.append_axes("right", size="5%", pad=0.1)  
+    fig.colorbar(im, ax=ax, cax = cax1)
+    plt.show()    
+    
+
+    
+    
+def show3D(x, title , **kwargs):
+        
+    # show slices for 3D
+    show_slices = kwargs.get('show_slices', [int(i/2) for i in x.shape])
+    
+    # defautl figure_size
+    figure_size = kwargs.get('figure_size', (10,5))    
+    
+    # font size of title and labels
+    cmap = kwargs.get('cmap', 'gray')
+    font_size = kwargs.get('font_size', [12, 12])
+
+    # Default minmax scaling
+    minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max())))
+    
+    labels = kwargs.get('labels', ['x','y','z'])     
+            
+    title_subplot = kwargs.get('title_subplot',['Axial','Coronal','Sagittal'])
+
+    fig, axs = plt.subplots(1, 3, figsize = figure_size)
+    
+    tmp = x.as_array()
+    
+    im1 = axs[0].imshow(tmp[show_slices[0],:,:], cmap=cmap, vmin=min(minmax), vmax=max(minmax))
+    axs[0].set_title(title_subplot[0], fontsize = font_size[0])
+    axs[0].set_xlabel(labels[0], fontsize = font_size[1])
+    axs[0].set_ylabel(labels[1], fontsize = font_size[1])
+    divider = make_axes_locatable(axs[0]) 
+    cax1 = divider.append_axes("right", size="5%", pad=0.1)      
+    fig.colorbar(im1, ax=axs[0], cax = cax1)   
+    
+    im2 = axs[1].imshow(tmp[:,show_slices[1],:], cmap=cmap, vmin=min(minmax), vmax=max(minmax))
+    axs[1].set_title(title_subplot[1], fontsize = font_size[0])
+    axs[1].set_xlabel(labels[0], fontsize = font_size[1])
+    axs[1].set_ylabel(labels[2], fontsize = font_size[1])
+    divider = make_axes_locatable(axs[1])  
+    cax1 = divider.append_axes("right", size="5%", pad=0.1)       
+    fig.colorbar(im2, ax=axs[1], cax = cax1)   
+
+    im3 = axs[2].imshow(tmp[:,:,show_slices[2]], cmap=cmap, vmin=min(minmax), vmax=max(minmax))
+    axs[2].set_title(title_subplot[2], fontsize = font_size[0]) 
+    axs[2].set_xlabel(labels[1], fontsize = font_size[1])
+    axs[2].set_ylabel(labels[2], fontsize = font_size[1])
+    divider = make_axes_locatable(axs[2])  
+    cax1 = divider.append_axes("right", size="5%", pad=0.1) 
+    fig.colorbar(im3, ax=axs[2], cax = cax1)       
+    
+    fig.suptitle(title, fontsize = font_size[0])
+    plt.tight_layout(h_pad=1)
+    plt.show()
+    
+         
+def show2D_channels(x, title, show_channels = [1], **kwargs):
+    
+    # defautl figure_size
+    figure_size = kwargs.get('figure_size', (10,5))    
+    
+    # font size of title and labels
+    cmap = kwargs.get('cmap', 'gray')
+    font_size = kwargs.get('font_size', [12, 12])
+    
+    labels = kwargs.get('labels', ['x','y'])
+
+    # Default minmax scaling
+    minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max()))) 
+    
+    if len(show_channels)==1:
+        show2D(x.subset(channel=show_channels[0]), title + ' Energy {}'.format(channel_to_energy(show_channels[0])) + " keV", **kwargs)        
+    else:
+        
+        fig, axs = plt.subplots(1, len(show_channels), sharey=True, figsize = figure_size)    
+    
+        for i in range(len(show_channels)):
+            im = axs[i].imshow(x.subset(channel=show_channels[i]).as_array(), cmap = cmap, vmin=min(minmax), vmax=max(minmax))
+            axs[i].set_title('Energy {}'.format(channel_to_energy(show_channels[i])) + "keV", fontsize = font_size[0])
+            axs[i].set_xlabel(labels[0], fontsize = font_size[1])
+            divider = make_axes_locatable(axs[i])
+            cax1 = divider.append_axes("right", size="5%", pad=0.1)    
+            fig.colorbar(im, ax=axs[i], cax = cax1)
+        axs[0].set_ylabel(labels[1], fontsize = font_size[1]) 
+        fig.suptitle(title, fontsize = font_size[0])
+        plt.tight_layout(h_pad=1)
+    plt.show()
+        
+def show3D_channels(x, title = None, show_channels = 0, **kwargs):
+    
+    show3D(x.subset(channel=show_channels), title + ' Energy {}'.format(channel_to_energy(show_channels))  + " keV", **kwargs)        
+        
+def show(x, title = None, show_channels = [1], **kwargs):
+    
+    sz = len(x.shape)
+    ch_num = x.geometry.channels
+    
+    if ch_num == 1:
+        
+        if sz == 2:
+            show2D(x, title, **kwargs)
+        elif sz == 3:
+            show3D(x, title, **kwargs)
+            
+    elif ch_num>1:
+        
+        if len(x.shape[1:]) == 2:
+            show2D_channels(x, title, show_channels,  **kwargs)
+            
+        elif len(x.shape[1:]) == 3:
+            show3D_channels(x, title, show_channels,  **kwargs)  
+    plt.show()
+            
+            
+        
+            
+if __name__ == '__main__':         
+    
+    from ccpi.framework import TestData, ImageData
+    import os
+    import sys
+    
+    loader = TestData(data_dir=os.path.join(sys.prefix, 'share','ccpi'))
+    data = loader.load(TestData.PEPPERS, size=(256,256))
+    ig = data.geometry
+    
+    show2D(data)
+       
+    if False:
+    
+        N = 100
+        ig2D = ImageGeometry(voxel_num_x=N, voxel_num_y=N)
+        ig3D = ImageGeometry(voxel_num_x=N, voxel_num_y=N, voxel_num_z=N)
+        
+        ch_number = 10
+        ig2D_ch = ImageGeometry(voxel_num_x=N, voxel_num_y=N, channels = ch_number)
+        ig3D_ch = ImageGeometry(voxel_num_x=N, voxel_num_y=N, voxel_num_z=N, channels = ch_number)
+        
+        x2D = ig2D.allocate('random_int')
+        x2D_ch = ig2D_ch.allocate('random_int')
+        x3D = ig3D.allocate('random_int')
+        x3D_ch = ig3D_ch.allocate('random_int')         
+         
+        #%%
+        ###############################################################################           
+        # test 2D cases
+        show(x2D)
+        show(x2D, title = '2D no font')
+        show(x2D, title = '2D with font', font_size = (50, 30))
+        show(x2D, title = '2D with font/fig_size', font_size = (20, 10), figure_size = (10,10))
+        show(x2D, title = '2D with font/fig_size', 
+                  font_size = (20, 10), 
+                  figure_size = (10,10),
+                  labels = ['xxx','yyy'])
+        ###############################################################################
+        
+        
+        #%%
+        ###############################################################################
+        # test 3D cases
+        show(x3D)
+        show(x3D, title = '2D no font')
+        show(x3D, title = '2D with font', font_size = (50, 30))
+        show(x3D, title = '2D with font/fig_size', font_size = (20, 20), figure_size = (10,4))
+        show(x3D, title = '2D with font/fig_size', 
+                  font_size = (20, 10), 
+                  figure_size = (10,4),
+                  labels = ['xxx','yyy','zzz'])
+        ###############################################################################
+        #%%
+        
+        ###############################################################################
+        # test 2D case + channel
+        show(x2D_ch, show_channels = [1, 2, 5])
+        
+        ###############################################################################
+                
+          
\ No newline at end of file
diff --git a/Wrappers/Python/ccpi/utilities/imagequality.py b/Wrappers/Python/ccpi/utilities/imagequality.py
new file mode 100644
index 0000000..392eaa7
--- /dev/null
+++ b/Wrappers/Python/ccpi/utilities/imagequality.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+# Copyright 2019 Science Technology Facilities Council
+# Copyright 2019 University of Manchester
+#
+# This work is part of the Core Imaging Library developed by Science Technology
+# Facilities Council and University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import print_function, division
+import numpy
+
+def psnr(img1, img2, data_range=1):
+    mse = numpy.mean( (img1 - img2) ** 2 )
+    if mse == 0:
+        return 1000
+    return 20 * numpy.log10(data_range / numpy.sqrt(mse))
+
+
diff --git a/Wrappers/Python/ccpi/utilities/jupyter/__init__.py b/Wrappers/Python/ccpi/utilities/jupyter/__init__.py
new file mode 100644
index 0000000..b87f813
--- /dev/null
+++ b/Wrappers/Python/ccpi/utilities/jupyter/__init__.py
@@ -0,0 +1,169 @@
+# imports for plotting
+from __future__ import print_function, division
+from ipywidgets import interact, interactive, fixed, interact_manual
+import ipywidgets as widgets
+import matplotlib.pyplot as plt
+from matplotlib import gridspec
+import numpy
+
+from IPython.display import HTML
+import random
+
+
+def display_slice(container, direction, title, cmap, minmax, size, axis_labels):
+    
+        
+    def get_slice_3D(x):
+        
+        if direction == 0:
+            img = container[x]
+            x_lim = container.shape[2]
+            y_lim = container.shape[1]
+            x_label = axis_labels[2]
+            y_label = axis_labels[1] 
+            
+        elif direction == 1:
+            img = container[:,x,:]
+            x_lim = container.shape[2]
+            y_lim = container.shape[0] 
+            x_label = axis_labels[2]
+            y_label = axis_labels[0]             
+            
+        elif direction == 2:
+            img = container[:,:,x]
+            x_lim = container.shape[1]
+            y_lim = container.shape[0]    
+            x_label = axis_labels[1]
+            y_label = axis_labels[0]             
+        
+        if size is None:
+            fig = plt.figure()
+        else:
+            fig = plt.figure(figsize=size)
+        
+        if isinstance(title, (list, tuple)):
+            dtitle = title[x]
+        else:
+            dtitle = title
+        
+        gs = gridspec.GridSpec(1, 2, figure=fig, width_ratios=(1,.05), height_ratios=(1,))
+        # image
+        ax = fig.add_subplot(gs[0, 0])
+      
+        ax.set_xlabel(x_label)     
+        ax.set_ylabel(y_label)
+ 
+        aximg = ax.imshow(img, cmap=cmap, origin='upper', extent=(0,x_lim,y_lim,0))
+        aximg.set_clim(minmax)
+        ax.set_title(dtitle + " {}".format(x))
+        # colorbar
+        ax = fig.add_subplot(gs[0, 1])
+        plt.colorbar(aximg, cax=ax)
+        plt.tight_layout()
+        plt.show(fig)
+        
+    return get_slice_3D
+
+    
+def islicer(data, direction, title="", slice_number=None, cmap='gray', minmax=None, size=None, axis_labels=None):
+
+    '''Creates an interactive integer slider that slices a 3D volume along direction
+    
+    :param data: DataContainer or numpy array
+    :param direction: slice direction, int, should be 0,1,2 or the axis label
+    :param title: optional title for the display
+    :slice_number: int start slice number, optional. If None defaults to center slice
+    :param cmap: matplotlib color map
+    :param minmax: colorbar min and max values, defaults to min max of container
+    :param size: int or tuple specifying the figure size in inch. If int it specifies the width and scales the height keeping the standard matplotlib aspect ratio 
+    '''
+    
+    if axis_labels is None:
+        if hasattr(data, "dimension_labels"):
+            axis_labels = [data.dimension_labels[0],data.dimension_labels[1],data.dimension_labels[2]]
+        else:
+            axis_labels = ['X', 'Y', 'Z']
+
+    
+    if hasattr(data, "as_array"):
+        container = data.as_array()
+        
+        if not isinstance (direction, int):
+            if direction in data.dimension_labels.values():
+                direction = data.get_dimension_axis(direction)                             
+
+    elif isinstance (data, numpy.ndarray):
+        container = data
+        
+    if slice_number is None:
+        slice_number = int(data.shape[direction]/2)
+        
+    slider = widgets.IntSlider(min=0, max=data.shape[direction]-1, step=1, 
+                             value=slice_number, continuous_update=False, description=axis_labels[direction])
+
+    if minmax is None:
+        amax = container.max()
+        amin = container.min()
+    else:
+        amin = min(minmax)
+        amax = max(minmax)
+    
+    if isinstance (size, (int, float)):
+        default_ratio = 6./8.
+        size = ( size , size * default_ratio )
+    
+    interact(display_slice(container, 
+                           direction, 
+                           title=title, 
+                           cmap=cmap, 
+                           minmax=(amin, amax),
+                           size=size, axis_labels=axis_labels),
+             x=slider);
+    
+    return slider
+    
+
+def link_islicer(*args):
+    '''links islicers IntSlider widgets'''
+    linked = [(widg, 'value') for widg in args]
+    # link pair-wise
+    pairs = [(linked[i+1],linked[i]) for i in range(len(linked)-1)]
+    for pair in pairs:
+        widgets.link(*pair)
+
+
+# https://stackoverflow.com/questions/31517194/how-to-hide-one-specific-cell-input-or-output-in-ipython-notebook/52664156
+
+def hide_toggle(for_next=False):
+    this_cell = """$('div.cell.code_cell.rendered.selected')"""
+    next_cell = this_cell + '.next()'
+
+    toggle_text = 'Toggle show/hide'  # text shown on toggle link
+    target_cell = this_cell  # target cell to control with toggle
+    js_hide_current = ''  # bit of JS to permanently hide code in current cell (only when toggling next cell)
+
+    if for_next:
+        target_cell = next_cell
+        toggle_text += ' next cell'
+        js_hide_current = this_cell + '.find("div.input").hide();'
+
+    js_f_name = 'code_toggle_{}'.format(str(random.randint(1,2**64)))
+
+    html = """
+        <script>
+            function {f_name}() {{
+                {cell_selector}.find('div.input').toggle();
+            }}
+
+            {js_hide_current}
+        </script>
+
+        <a href="javascript:{f_name}()">{toggle_text}</a>
+    """.format(
+        f_name=js_f_name,
+        cell_selector=target_cell,
+        js_hide_current=js_hide_current, 
+        toggle_text=toggle_text
+    )
+
+    return HTML(html)    
\ No newline at end of file
diff --git a/Wrappers/Python/setup.py b/Wrappers/Python/setup.py
index ea6181e..ed2cd25 100644
--- a/Wrappers/Python/setup.py
+++ b/Wrappers/Python/setup.py
@@ -35,6 +35,7 @@ setup(
               'ccpi.optimisation.algorithms',
               'ccpi.optimisation.functions',
               'ccpi.processors',
+              'ccpi.utilities', 'ccpi.utilities.jupyter',
               'ccpi.contrib','ccpi.contrib.optimisation',
               'ccpi.contrib.optimisation.algorithms'],
     data_files = [('share/ccpi', ['data/boat.tiff',