using Will's Figure infra

test/integration/test_figure.py

@@ -0,0 +1,172 @@
+# Copyright (C) 2023 The Jackson Laboratory
+# All rights reserved.
+#
+# Use is subject to license terms supplied in LICENSE.
+
+from omero_cli_transfer import TransferControl
+from cli import CLITest
+from omero.gateway import BlitzGateway
+
+import ezomero
+import pytest
+import os
+import tarfile
+import json
+
+
+class TestFigure(CLITest):
+
+    def setup_method(self, method):
+        super(TestFigure, self).setup_method(method)
+        self.cli.register("transfer", TransferControl, "TEST")
+        self.args += ["transfer"]
+        self.idonly = "-1"
+        self.imageid = "Image:-1"
+        self.datasetid = "Dataset:-1"
+        self.projectid = "Project:-1"
+        self.plateid = "Project:-1"
+        self.screenid = "Project:-1"
+        self.gw = BlitzGateway(client_obj=self.client)
+
+    def create_image(self, sizec=4, sizez=1, sizet=1, target_name=None):
+        images = self.import_fake_file(
+                images_count=2, sizeZ=sizez, sizeT=sizet, sizeC=sizec,
+                client=self.client)
+        images.append(self.create_test_image(100, 100, 1, 1, 1,
+                                             self.client.getSession()))
+        self.imageid = "Image:%s" % images[0].id.val
+        self.source = "Image:%s" % images[1].id.val
+        for image in images:
+            img = self.gw.getObject("Image", image.id.val)
+            img.getThumbnail(size=(96,), direct=False)
+        if target_name == "datasetid" or target_name == "projectid" or\
+           target_name == "idonly":
+            # Create Project/Dataset hierarchy
+            project = self.make_project(client=self.client)
+            self.project = self.gw.getObject("Project", project.id.val)
+            dataset = self.make_dataset(client=self.client)
+            self.dataset = self.gw.getObject("Dataset", dataset.id.val)
+            self.projectid = "Project:%s" % self.project.id
+            self.datasetid = "Dataset:%s" % self.dataset.id
+            self.idonly = "%s" % self.project.id
+            self.link(obj1=project, obj2=dataset)
+            for i in images:
+                self.link(obj1=dataset, obj2=i)
+
+    def delete_all(self):
+        pjs = self.gw.getObjects("Project")
+        for p in pjs:
+            pj_id = p.id
+            print(f"deleting project {pj_id}")
+            self.gw.deleteObjects("Project", [pj_id], deleteAnns=True,
+                                  deleteChildren=True, wait=True)
+        ds = self.gw.getObjects("Dataset")
+        for d in ds:
+            ds_id = d.id
+            print(f"deleting dataset {ds_id}")
+            self.gw.deleteObjects("Dataset", [ds_id], deleteAnns=True,
+                                  deleteChildren=True, wait=True)
+        scs = self.gw.getObjects("Screen")
+        for sc in scs:
+            sc_id = sc.id
+            print(f"deleting screen {sc_id}")
+            self.gw.deleteObjects("Screen", [sc_id], deleteAnns=True,
+                                  deleteChildren=True, wait=True)
+        pls = self.gw.getObjects("Plate")
+        for pl in pls:
+            pl_id = pl.id
+            print(f"deleting plate {pl_id}")
+            self.gw.deleteObjects("Plate", [pl_id], deleteAnns=True,
+                                  deleteChildren=True, wait=True)
+        ims = self.gw.getObjects("Image")
+        im_ids = []
+        for im in ims:
+            im_ids.append(im.id)
+            print(f"deleting image {im.id}")
+        if im_ids:
+            self.gw.deleteObjects("Image", im_ids, deleteAnns=True,
+                                  deleteChildren=True, wait=True)
+
+    def get_panel_json(image, index, page_x):
+        """Create a panel."""
+        channel = {'emissionWave': "400",
+                   'label': "DAPI",
+                   'color': "0000FF",
+                   'inverted': False,
+                   'active': True,
+                   'window': {'min': 0,
+                              'max': 255,
+                              'start': 0,
+                              'end': 255},
+                   }
+
+        pix = image.getPrimaryPixels()
+        size_x = pix.getSizeX().val
+        size_y = pix.getSizeY().val
+        # shapes coordinates are Image coordinates
+        # Red Line diagonal from corner to corner
+        # Arrow from other corner to centre
+        shapes = [{"type": "Rectangle", "x": size_x/4, "y": size_y/4,
+                   "width": size_x/2, "height": size_y/2,
+                   "strokeWidth": 4, "strokeColor": "#FFFFFF"},
+                  {"type": "Line", "x1": 0, "x2": size_x, "y1": 0,
+                   "y2": size_y, "strokeWidth": 5, "strokeColor": "#FF0000"},
+                  {"type": "Arrow", "x1": 0, "x2": size_x/2, "y1": size_y,
+                   "y2": size_y/2, "strokeWidth": 10, "strokeColor": "#FFFF00"},
+                  {"type": "Ellipse", "x": size_x/2, "y": size_y/2,
+                   "radiusX": size_x/3, "radiusY": size_y/2, "rotation": 45,
+                   "strokeWidth": 10, "strokeColor": "#00FF00"}]
+
+        # This works if we have Units support (OMERO 5.1)
+        px = image.getPrimaryPixels().getPhysicalSizeX()
+        py = image.getPrimaryPixels().getPhysicalSizeY()
+        pz = image.getPrimaryPixels().getPhysicalSizeZ()
+        img_json = {
+            "imageId": image.getId().getValue(),
+            "name": "test_image",  # image.getName().getValue()
+            "width": 100 * (index + 1),
+            "height": 100 * (index + 1),
+            "sizeZ": pix.getSizeZ().val,
+            "theZ": 0,
+            "sizeT": pix.getSizeT().val,
+            "theT": 0,
+            # rdef -> used at panel creation then deleted
+            "channels": [channel],
+            "orig_width": size_x,
+            "orig_height": size_y,
+            "x": page_x,
+            "y": index * 200,
+            'datasetName': "TestDataset",
+            'datasetId': 123,
+            'pixel_size_x': None if px is None else px.getValue(),
+            'pixel_size_y': None if py is None else py.getValue(),
+            'pixel_size_z': None if pz is None else pz.getValue(),
+            'pixel_size_x_symbol': '\xB5m' if px is None else px.getSymbol(),
+            'pixel_size_z_symbol': None if pz is None else pz.getSymbol(),
+            'pixel_size_x_unit': None if px is None else str(px.getUnit()),
+            'pixel_size_z_unit': None if pz is None else str(pz.getUnit()),
+            'deltaT': [],
+            "zoom": 100 + (index * 50),
+            "dx": 0,
+            "dy": 0,
+            "rotation": 100 * index,
+            "rotation_symbol": '\xB0',
+            "max_export_dpi": 1000,
+            "shapes": shapes,
+        }
+        return img_json
+
+    def create_figure(self, images):
+        """Create JSON to export figure."""
+        figure_json = {"version": 2,
+                       "paper_width": 595,
+                       "paper_height": 842,
+                       "page_size": "A4",
+                       }
+        panels = []
+        for idx, image in enumerate(images):
+            panels.append(self.get_panel_json(image, 0, 50 + (idx * 300)))
+            panels.append(self.get_panel_json(image, 1, 50 + (idx * 300)))
+        figure_json['panels'] = panels
+        json_string = json.dumps(figure_json)
+        return json_string

test/integration/test_transfer.py

@@ -149,6 +149,7 @@ def test_pack(self, target_name, tmpdir):
                 self.cli.invoke(args, strict=True)
         self.delete_all()
 
+
     @pytest.mark.parametrize('target_name', sorted(SUPPORTED))
     def test_pack_special(self, target_name, tmpdir):
         if target_name == "datasetid" or target_name == "projectid" or\