Tornado server

requirements.txt

@@ -1,4 +1,5 @@
 numpy>=1.6
 nose>=1.2
+tornado>=3.1
 nibabel>=2.0
 numpydoc

scripts/sliced_probmap_viz

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+from pylab import *
+import nibabel
+import sys
+from itertools import izip
+
+import argparse
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Superimposed slices viz')
+    parser.add_argument('-s', dest='slices', type=float, nargs='+',
+                        help='Slices to show')#, required=True)
+    parser.add_argument('-i', dest='base_image', type=str,
+                        help='base image to show')#, required=True)
+    parser.add_argument('-j', dest='tract_image', type=str, nargs='+',
+                        help='tract image to show')#, required=True)
+    parser.add_argument('-o', dest='output', type=str,
+                        help='output image')#, required=True)
+    parser.add_argument('--invert', dest='inverse_order',
+                        action='store_true', help='invert the slice order')
+    parser.add_argument('--step', dest='step',
+                        action='store_true', help='Take the slices as `start end step`')
+    parser.add_argument('-t', dest='threshold', type=float, default=0,
+                        help='lower threshold of the tract image')
+    parser.add_argument('--axis', dest='axis', type=int, default=2,
+                        help='axis of the slices')
+    parser.add_argument('--mip', dest='mip', action='store_true',
+                        help='show maximum intensity projections')
+
+    parser.add_argument('--mm', dest='mm', action='store_true',
+                        help='slices are in millimeters')
+
+
+    parser.add_argument(
+        '--displacement', dest='displacement', type=float, default=.1,
+        help='displacement between axes between 0. and 1.')
+    parser.add_argument(
+        '--displacement_direction', dest='displacement_direction', type=str,
+        choices=('row', 'col'), default='row',
+        help='displacement direction: "row" or "col"')
+    parser.add_argument('--color', dest='color', type=str, nargs='+',
+                        default='YlOrRd_r', help='Coloring for the tract (default %(default)s)')
+    parser.add_argument('--alpha', dest='alpha', type=float, nargs='+', default=1.,
+                        help='Alpha for the probability maps')
+
+    parser.add_argument('--print-colors', dest='print_colors', action='store_true',
+                        help='Print the list of colormaps')
+
+    args = parser.parse_args()
+
+    if args.print_colors:
+        from matplotlib import colors
+        maps = [
+            cm_ for cm_ in dir(cm)
+            if isinstance(getattr(cm, cm_), colors.Colormap)
+        ]
+        max_length = max(len(cm_) for cm_ in maps) + 3
+        str_ = "{:<" + str(max_length) + "}"
+        for i in xrange(0, len(maps), 4):
+            maps_ = maps[i: i + 4]
+            str_line = str_ * len(maps_)
+            print str_line.format(*maps_)
+        parser.exit(0)
+
+    fig = figure(frameon=False)
+    fa_img = nibabel.load(args.base_image)
+    fa = fa_img.get_data()
+
+    if isinstance(args.tract_image, str):
+        args.tract_image = [args.tract_image]
+    tracts = [nibabel.load(tract_image).get_data() for tract_image in args.tract_image]
+
+    if isinstance(args.alpha, float):
+        args.alpha = [args.alpha]
+    if len(args.alpha) == 1:
+        args.alpha *= len(tracts)
+
+    if isinstance(args.color, str):
+        args.color = [args.color]
+    if len(args.color) == 1:
+        args.color *= len(tracts)
+
+    t_colormap = []
+    for colormap in args.color:
+        t_colormap.append(getattr(cm, colormap))
+        t_colormap[-1].set_under(alpha=0)
+
+    fa_cm = cm.gray
+    fa_cm.set_under(alpha=0)
+
+    if args.step:
+        args.slices = np.linspace(args.slices[0], args.slices[1], (args.slices[1] - args.slices[0]) / args.slices[2])
+
+    if args.mm:
+        ras_pos = zeros(4)
+        ras_pos[-1] = 1.
+        if any(np.diag(np.diag(fa_img.get_affine()[:3, :3])) != fa_img.get_affine()[:3, :3]):
+                raise ValueError("Affine matrix is not diagonal, we don't handle this case")
+        for i, s in enumerate(args.slices):
+            ras_pos[args.axis] = s
+            ijk_pos = np.linalg.solve(fa_img.get_affine(), ras_pos)
+            args.slices[i] = int(round(ijk_pos[args.axis]))
+    else:
+            args.slices = [int(s) for s in args.slices]
+
+    for i, y in enumerate(args.slices):
+        if args.inverse_order:
+            pos = len(args.slices) - 1 - i
+        else:
+            pos = i
+
+        if args.displacement_direction == 'row':
+            fig.add_axes([pos * args.displacement, 0, .5, .5], frameon=False)
+        else:
+            fig.add_axes([0, pos * args.displacement, .5, .5], frameon=False)
+        ax = gca()
+        ax.hold(True)
+
+        slices = [slice(None)] * 3
+        slices[args.axis] = y
+        slices = tuple(slices)
+
+        imshow(fa[slices].T, cmap=fa_cm, vmin=min(1e-10, fa[slices].min), origin=True, interpolation='spline36')
+        for tract, colormap in izip(tracts, t_colormap):
+            thr = min(tract.max() - 1e-10, args.threshold)
+            if args.mip:
+                tract_slice = tract.max(args.axis).T
+            else:
+                tract_slice = tract[slices].T
+            imshow(
+                tract_slice, cmap=colormap,
+                vmin=thr, vmax=tract.max(), origin=True, interpolation='gaussian'
+            )
+        xticks([])
+        yticks([])
+        ax.hold(False)
+    savefig(args.output, bbox_inches='tight', transparent=True, pad_inches=0)
+
+
+if __name__ == '__main__':
+    sys.exit(main())

scripts/tract_math

@@ -31,7 +31,7 @@ def tract_math_operation(help_text, needs_one_tract=True):
 
 
 def main():
-    from tract_querier.tract_math import operations
+    from tract_querier.tract_math import tract_math_operations as operations
     from tract_querier.tract_math import TractMathWrongArgumentsError
 
     usage = r"""

scripts/tract_querier

@@ -39,6 +39,25 @@ def main():
         help="Bounding box to apply to the image affine transform and tracts "
         "to put both in AC-PC coordinate space"
     )
+    parser.add_option(
+        '--interactive-webdisplay', dest='interactive_web', action='store_true',
+        help='Enables interactive display of the results'
+    )
+    parser.add_option(
+        '--interactive-colortable', dest='interactive_colortable', type=str,
+        help='Atlas colortable for the webgl viz'
+    )
+    parser.add_option(
+        '--interactive-webdisplay-hostname', dest='interactive_hostname',
+        help='Server port for the interactive display of the results: default: $(default)s',
+        default='localhost'
+    )
+
+    parser.add_option(
+        '--interactive-webdisplay-port', dest='interactive_port',
+        help='Server port for the interactive display of the results: default $(default)04d',
+        default=9999
+    )
 
     (options, args) = parser.parse_args()
 
@@ -61,6 +80,9 @@ def main():
 
     import tract_querier
 
+    if options.interactive_web:
+        options.interactive = True
+
     if options.bounding_box_affine_transform:
         try:
             bounding_box_affine_transform = np.fromstring(
@@ -139,7 +161,19 @@ def main():
         options.tractography_file_name
     )
 
-    tractography_extension = os.path.splitext(options.tractography_file_name)[-1]
+    input_split = os.path.splitext(options.tractography_file_name)
+    output_split = os.path.splitext(options.output_file_name)
+    if len(output_split) > 1:
+        options.output_file_name = output_split[0]
+        tractography_extension = output_split[1]
+
+    if options.interactive_web is not None and tractography_extension != '.trk':
+        print (
+            "The web application only works with Trackvis output files"
+            " setting the output to Trackvis mode"
+        )
+        tractography_extension = '.trk'
+
     if tractography_extension == '.trk':
         tractography_extra_kwargs = {
             'affine': tr.affine,
@@ -203,13 +237,11 @@ def main():
                 extension=tractography_extension, extra_kwargs=tractography_extra_kwargs
             )
     else:
-        query_save = (
-            lambda query_name, query_result:
-            save_query(
+        def query_save(query_name, query_result):
+            return save_query(
                 query_name, tr, options, {query_name: query_result},
                 extension=tractography_extension, extra_kwargs=tractography_extra_kwargs
             )
-        )
 
         interactive_shell = tract_querier.TractQuerierCmd(
             tractography_spatial_indexing,
@@ -218,7 +250,10 @@ def main():
             include_folders=qry_search_folders
         )
 
-        interactive_shell.cmdloop()
+        if options.interactive_web:
+            activate_webserver(options, interactive_shell)
+        else:
+            interactive_shell.cmdloop()
 
 
 def save_query(query_name, tractography, options, evaluated_queries, extension='.vtk', extra_kwargs={}):
@@ -272,6 +307,33 @@ def save_tractography_file(
     )
 
 
+def activate_webserver(options, shell):
+    import os
+    from tract_querier import tornado_server
+    from uuid import uuid4
+    suffix = str(uuid4()).replace('-', '')
+    options.interactive = True
+
+    options.interactive_port = int(options.interactive_port)
+
+    print "Starting web server, please direct your browser to http://%s:%04d" % (
+        options.interactive_hostname,
+        options.interactive_port
+    )
+
+    tornado_server.xtk_server(
+        atlas=os.path.abspath(options.atlas_file_name),
+        colortable=options.interactive_colortable,
+        hostname=options.interactive_hostname,
+        port=options.interactive_port,
+        files_path=os.getcwd(),
+        suffix=suffix,
+        shell=shell
+    )
+
+
+
+
 def affine_transform_tract(affine_transform, tract):
     import numpy as np
 

setup.py

@@ -24,6 +24,17 @@ def configuration(parent_package='', top_path=None):
 
 
 if __name__ == "__main__":
+    requires_base = open('requirements.txt').readlines()
+    requires = []
+    for i, req in enumerate(requires_base):
+        if req.strip().startswith('#') or req.strip().startswith('-'):
+            continue
+        req = req.strip()
+        if '>' in req:
+            req = req.replace('>', '(>')
+            req += ')'
+        requires.append(req)
+
     setup(
         name=DISTNAME,
         maintainer=MAINTAINER,
@@ -34,10 +45,7 @@ def configuration(parent_package='', top_path=None):
         version=VERSION,
         download_url=DOWNLOAD_URL,
         long_description=LONG_DESCRIPTION,
-        requires=[
-            'numpy(>=1.6)',
-            'nibabel(>=1.3)'
-        ],
+        requires=requires,
         classifiers=[
             'Intended Audience :: Science/Research',
             'Programming Language :: Python',
@@ -49,7 +57,8 @@ def configuration(parent_package='', top_path=None):
         ],
         scripts=[
             'scripts/tract_querier',
-            'scripts/tract_math'
+            'scripts/tract_math',
+            'scripts/sliced_probmap_viz',
         ],
         **(configuration().todict())
     )

tract_querier/setup.py

@@ -9,6 +9,7 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('code_util')
     config.add_subpackage('tensor')
     config.add_subpackage('nipype')
+    config.add_subpackage('tornado_server')
     config.add_data_files(('queries', [
         'data/FreeSurfer.qry',
         'data/JHU_MNI_SS_WMPM_Type_I.qry',