Added initial support for slide-to-slide reg

setup.py

 import setuptools
 
-from slider import __version__
-
 with open('requirements.txt', 'rt') as f:
     install_requires = [l.strip() for l in f.readlines()]
 
 setuptools.setup(
     name="slider",
-    version=__version__,
+    version='0.0.1',
     author="Sean Fitzgibbon",
     author_email="sean.fitzgibbon@ndcn.ox.ac.uk",
     description="Slide Registration tool",
     url="https://git.fmrib.ox.ac.uk/seanf/slider",
     install_requires=install_requires,
-    scripts=['slider.py'],
+    scripts=['slider_app.py'],
     packages=setuptools.find_packages(),
     include_package_data=True,
     python_requires='>=3.7',

slider.py

-#!/usr/bin/env python
-
-
-
-
-
-if __name__ == "__main__":
-    pass
\ No newline at end of file

slider/__init__.py

-__version__ = '0.0.1'
\ No newline at end of file

slice-register.py → slider/slide_reg.py

@@ -68,8 +68,7 @@
 
 
 """
-Oxford Post-Mortem MND Biomarkers Histology-MRI Registration Pipeline, Stage 1:
-Registers a histology slide to the corresponding tissue block photograph.
+Register 2D-slide to 2D-slide
 
 After the input images are centralised, the registration employs sequential
 rigid, affine and non-linear alignment. Depending on the chosen direction of
@@ -92,8 +91,6 @@ optimised:
     offset:
         [centralisation]
 
-The above chain maps the full-resolution 2D histology coordinates to the 2D
-space of the tissue block photograph.
 
 """
 
@@ -868,75 +865,71 @@ def pad(timg, **kwargs):
     # PROGRAM FLOW CONTROL
 
 
-def slide_to_slide(args):
+def register_slide_to_slide(moving, fixed, out, config):
     """
-    Main program code. Controls program flow, handles command-line arguments.
+    Register 2D-slide to 2D-slide using TIRL.
 
     """
-    cnf = args.config
-    if os.path.isfile(cnf):
-        with open(cnf, "r") as fp:
-            cnf = dict(json.load(fp))
+
+    if os.path.isfile(config):
+        with open(config, "r") as fp:
+            config = dict(json.load(fp))
     else:
         raise FileNotFoundError(f"The provided configuration file "
-                                f"does not exist: {args.config}")
-
-    # Override histology and block file paths in the configuration file with
-    # those provided on the command line.
-    if args.moving and os.path.isfile(args.moving):
-        cnf["moving"]["file"] = args.moving
-    if args.fixed and os.path.isfile(args.fixed):
-        cnf["fixed"]["file"] = args.fixed
-    if args.out:
-        cnf["general"]["outputdir"] = args.out
-        cnf["general"]["logfile"] = f'{args.out}/logfile.log'
-        cnf["general"]["paramlogfile"] = f'{args.out}/paramlog.log'
-
-    # Override verbose option in configurations
-    cnf["general"]["verbose"] = args.verbose
+                                f"does not exist: {config}")
 
-    # Run registration script
-    run(cnf)
+    config["moving"]["file"] = moving
+    config["fixed"]["file"] = fixed
+    config["general"]["outputdir"] = out
+    config["general"]["logfile"] = f'{out}/logfile.log'
+    config["general"]["paramlogfile"] = f'{out}/paramlog.log'
 
+    # # Override verbose option in configurations
+    # cnf["general"]["verbose"] = args.verbose
 
-def create_cli(parser):
-    """
-    Sets up the CLI argument parser instance.
-
-    """
-    parser.add_argument("--moving", metavar="image",
-                        help="Moving slide", default=None, type=str,
-                        required=True)
-    parser.add_argument("--fixed", metavar="image",
-                        help="Fixed slide", default=None, type=str,
-                        required=True)
-    parser.add_argument("--out", metavar="dir",
-                        help="Output directory", default=None, type=str,
-                        required=True)
-    parser.add_argument("--config", metavar="cnf_file.json",
-                        help="configuration file", default='default.json', type=str,
-                        required=False)
-    parser.add_argument("-v", "--verbose", default=False, action="store_true",
-                        help="Print status messages to the command line",
-                        required=False)
-
-    return parser
-
-
-def main(*args):
-    """ Main program code. """
-
-    parser = argparse.ArgumentParser(
-        prog="slice-register.py",
-        description="Registers a histology slide to "
-                    "another histology slide.")
-    parser = create_cli(parser)
-
-    if args:
-        slide_to_slide(parser.parse_args(args))
-    else:
-        parser.print_help()
-
-
-if __name__ == "__main__":
-    main(*sys.argv[1:])
+    # Run registration script
+    # print(config)
+    run(config)
+
+
+# def create_cli(parser):
+#     """
+#     Sets up the CLI argument parser instance.
+
+#     """
+#     parser.add_argument("--moving", metavar="image",
+#                         help="Moving slide", default=None, type=str,
+#                         required=True)
+#     parser.add_argument("--fixed", metavar="image",
+#                         help="Fixed slide", default=None, type=str,
+#                         required=True)
+#     parser.add_argument("--out", metavar="dir",
+#                         help="Output directory", default=None, type=str,
+#                         required=True)
+#     parser.add_argument("--config", metavar="cnf_file.json",
+#                         help="configuration file", default='default.json', type=str,
+#                         required=False)
+#     parser.add_argument("-v", "--verbose", default=False, action="store_true",
+#                         help="Print status messages to the command line",
+#                         required=False)
+
+#     return parser
+
+
+# def main(*args):
+#     """ Main program code. """
+
+#     parser = argparse.ArgumentParser(
+#         prog="slice-register.py",
+#         description="Registers a histology slide to "
+#                     "another histology slide.")
+#     parser = create_cli(parser)
+
+#     if args:
+#         register_slide_to_slide(parser.parse_args(args))
+#     else:
+#         parser.print_help()
+
+
+# if __name__ == "__main__":
+#     main(*sys.argv[1:])

slider_app.py

+#!/usr/bin/env python
+import argparse
+import sys
+
+from slider.slide_reg import register_slide_to_slide
+
+def add_slide_cli(subparsers):
+    """
+    Set up slide-to-slide subparser instance.
+    """
+    parser = subparsers.add_parser(
+        'SLIDE',
+        description='Register 2D slide to 2D slide',
+        formatter_class=lambda prog: argparse.HelpFormatter(prog, max_help_position=55, width=100)
+    )
+
+    parser.add_argument("moving", metavar="<moving>",
+                        help="Moving slide", type=str)
+    parser.add_argument("fixed", metavar="<fixed>",
+                        help="Fixed slide", type=str)
+    parser.add_argument("--out", metavar="<dir>",
+                        help="Output directory", default=None, type=str,
+                        required=False)
+    parser.add_argument("--config", metavar="<default.json>",
+                        help="configuration file", default='default.json', type=str,
+                        required=False)
+    # parser.add_argument("-v", "--verbose", default=False, action="store_true",
+    #                     help="Print status messages to the command line",
+    #                     required=False)
+    parser.set_defaults(method='slide')
+
+
+def add_chart_cli(subparsers):
+    """
+    Set up chart-to-slide subparser instance.
+    """
+    parser = subparsers.add_parser(
+        'CHART',
+        description='Register charting to 2D slide',
+        formatter_class=lambda prog: argparse.HelpFormatter(prog, max_help_position=55, width=100)
+    )
+    parser.set_defaults(method='chart')
+
+
+
+if __name__ == "__main__":
+    """ Main program code. """
+
+    parser = argparse.ArgumentParser()
+
+    subparsers = parser.add_subparsers()
+    add_slide_cli(subparsers)
+    add_chart_cli(subparsers)
+
+    # ---
+
+    if len(sys.argv) == 1:
+        parser.parse_args(['-h'])
+    else:
+        args = vars(parser.parse_args())
+
+    method = args.pop('method')
+
+    if method == 'slide':
+        register_slide_to_slide(**args)
+    elif method == 'chart':
+        pass
+    else:
+        raise RuntimeError(f'Unknown method: {method}')