Add channels to pointMatchClient (#144)

* Add channels to def pointMatchClient() and get_canvas_url_template().

* Add scale as an option.

* Remove scale from pointMatchClient.  Can use SiftPointMatchOptions.renderScale instead.

* Basic test to test multiple channels with pointmatch client.

* Assert for fewer pointmatches, not none, with different channels.

* Add test for different channel order.

* Tweaked tests & docs.

* Remove scale from get_canvas_url_template.

* Actually remove scale from get_canvas_url_template.

integration_tests/test_multichannel.py

@@ -3,6 +3,7 @@
 import pytest
 import logging
 import sys
+import numpy as np
 
 root = logging.getLogger()
 root.setLevel(logging.DEBUG)
@@ -33,8 +34,81 @@ def multichannel_test_stack(render):
     return stack
 
 
+@pytest.fixture(scope='module')
+def multichannel_test_stack_channelflip(render):
+    stack = 'multichannel_test_channelflip'
+    tilespecs = [renderapi.tilespec.TileSpec(json=d)
+                 for d in test_2_channels_d]
+    for tilespec in tilespecs:
+        tilespec.channels.reverse()
+    renderapi.stack.create_stack(stack, render=render)
+    renderapi.client.import_tilespecs(stack, tilespecs, render=render)
+    renderapi.stack.set_stack_state(stack, 'COMPLETE', render=render)
+    return stack
+
+
+@pytest.fixture(scope='module')
+def test_pm_collection(render):
+    collection = 'test_multichan_collection'
+    renderapi.pointmatch.import_matches(
+        collection, test_matches, render=render)
+    return collection
+
+
 def test_section_image_channels(render, multichannel_test_stack):
     section_image = renderapi.image.get_section_image(multichannel_test_stack,
                                                       1.0, channel='DAPI',
                                                       render=render)
     print(section_image.shape)
+
+
+def test_section_image_same_channel_different_channel_order(render, multichannel_test_stack, multichannel_test_stack_channelflip):
+    section_image = renderapi.image.get_section_image(multichannel_test_stack,
+                                                      1.0, channel='DAPI',
+                                                      render=render)
+    section_image2 = renderapi.image.get_section_image(multichannel_test_stack_channelflip,
+                                                      1.0, channel='DAPI',
+                                                      render=render)
+    assert(np.array_equal(section_image, section_image2))
+
+
+def test_section_image_different_channel_order(render, multichannel_test_stack, multichannel_test_stack_channelflip):
+    section_image = renderapi.image.get_section_image(multichannel_test_stack,
+                                                      1.0,
+                                                      render=render)
+    section_image2 = renderapi.image.get_section_image(multichannel_test_stack_channelflip,
+                                                      1.0,
+                                                      render=render)
+    assert(not np.array_equal(section_image, section_image2))
+
+
+def test_multichannel_pointmatches(render, multichannel_test_stack):
+    collection = 'test_multichannel_pointmatch_same_channel'
+    sift_options = renderapi.client.SiftPointMatchOptions(renderScale=0.5)
+    tile_pairs = [['100000001003000', '100000001004000']]
+    renderapi.client.pointMatchClient(multichannel_test_stack,
+                    collection,
+                    tile_pairs,
+                    filter=True,
+                    excludeAllTransforms=True,
+                    stackChannels='DAPI',
+                    sift_options=sift_options,
+                    render=render)
+    pms1 = renderapi.pointmatch.get_matches_involving_tile(
+        collection, collection, '100000001003000', render=render)
+    assert(len(pms1) > 0)
+
+    collection2 = 'test_multichannel_pointmatch_different_channel'
+    renderapi.client.pointMatchClient(multichannel_test_stack,
+                    collection2,
+                    tile_pairs,
+                    stack2=multichannel_test_stack,
+                    filter=True,
+                    excludeAllTransforms=True,
+                    stackChannels='DAPI',
+                    stack2Channels='TdTomato',
+                    sift_options=sift_options,
+                    render=render)            
+    with pytest.raises(renderapi.errors.RenderError):      
+        pms2 = renderapi.pointmatch.get_matches_involving_tile(
+            collection2, collection2, '100000001003000', render=render)

renderapi/client/client_calls.py

@@ -474,6 +474,7 @@ def get_canvas_url_template(
         stack, filter=False, renderWithoutMask=False,
         normalizeForMatching=True, excludeTransformsAfterLast=None,
         excludeFirstTransformAndAllAfter=None, excludeAllTransforms=False,
+        channels=None,
         host=None, port=None, owner=None, project=None, client_script=None,
         render=None, **kwargs):
     """function for making a render-parameters url template for point matching
@@ -507,6 +508,11 @@ def get_canvas_url_template(
     excludeAllTransforms: bool
         alternative to normalizeForMatching which simply removes all transforms from the list.
         default=False
+    channels: str
+        list of channels and weights to render in the format [channel name], [channel name]__[weight] or
+        channel one name]__[weight]__ ... [channel n name]__[weight].
+        e.g., "DAPI" or "DAPI__0.9__TdTomato__0.1"
+        default = None
     """  # noqa: E501
     request_url = format_preamble(host, port, owner, project, stack)
     tile_base_url = request_url + "/tile"
@@ -534,6 +540,8 @@ def get_canvas_url_template(
             excludeFirstTransformAndAllAfter)
     if excludeAllTransforms:
         url_suffix += '&excludeAllTransforms=true'
+    if channels:
+        url_suffix += '&channels={}'.format(channels)
 
     canvas_url_template = "%s/{}/%s" % (tile_base_url,
                                         url_suffix)
@@ -551,6 +559,8 @@ def pointMatchClient(stack, collection, tile_pairs,
                      excludeTransformsAfterLast=None,
                      excludeAllTransforms=None,
                      excludeFirstTransformAndAllAfter=None,
+                     stackChannels=None,
+                     stack2Channels=None,
                      subprocess_mode=None,
                      host=None, port=None,
                      owner=None, project=None, client_script=None,
@@ -598,7 +608,13 @@ def pointMatchClient(stack, collection, tile_pairs,
         transforms that you had applied after it. default= None.
     excludeAllTransforms: bool
         alternative to normalizeForMatching which simply removes all transforms from the list.
-        default=False
+        default = False
+    stackChannels: str or None
+        If specified, option to select which channel is used for the stack.
+        default = None
+    stack2Channels: str or None
+        If specified, option to select which channel is used for stack2, if specified.
+        default = None
 
     """  # noqa: E501
     sift_options = (SiftPointMatchOptions(**kwargs) if sift_options is None
@@ -625,6 +641,7 @@ def pointMatchClient(stack, collection, tile_pairs,
         excludeTransformsAfterLast,
         excludeFirstTransformAndAllAfter,
         excludeAllTransforms,
+        channels=stackChannels,
         host=host,
         port=port,
         owner=owner,
@@ -640,14 +657,14 @@ def pointMatchClient(stack, collection, tile_pairs,
             excludeTransformsAfterLast,
             excludeFirstTransformAndAllAfter,
             excludeAllTransforms,
+            channels=stack2Channels,
             host=host,
             port=port,
             owner=owner,
             project=project,
             client_script=client_script)
     else:
         canvas_url_template2 = canvas_url_template
-
     for tile1, tile2 in tile_pairs:
         argvs += [canvas_url_template.format(tile1),
                   canvas_url_template2.format(tile2)]