René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Example code only works for square image [bug]","articleBody":"## Expected behavior\r\n`segmentify` should work for non-square images (width != length, ex. 512x512 is square, 511x512 is not square)\r\n\r\n## Potentially relevant issues/PR\r\n#11 #13 \r\n\r\n## How to reproduce the bug\r\nBelow is a slightly modified version of https://github.com/transformify-plugins/segmentify/blob/master/examples/launch.py  \r\n1. Run the code as is, popping the napari window; click `execute` button, confirm working\r\n2. Un-comment the two lines right before `napari.gui_qt`; run the code, popping the napari window, click `execute` button, and confirm it crashes\r\n```\r\nimport os\r\nimport napari\r\nfrom segmentify import segmentation\r\nimport numpy as np\r\nfrom skimage import io\r\n\r\n\r\n# parse input file\r\nexample_image = os.path.join(os.path.abspath(os.path.dirname(__file__)), \"hpa.png\")\r\nexample_labels = os.path.join(os.path.abspath(os.path.dirname(__file__)), \"hpa_labels.tif\")\r\n\r\nexample_image = io.imread(example_image)\r\nexample_labels = io.imread(example_labels)\r\n\r\n### WARNING: uncomment these two lines below to reproduce bug ###\r\n#example_image = example_image[:, 1:]\r\n#example_labels = example_labels[:, 1:]\r\n##########################################################\r\n\r\nwith napari.gui_qt():\r\n    viewer = napari.Viewer()\r\n\r\n    # instantiate the widget\r\n    gui = segmentation.Gui()\r\n\r\n    # add our new widget to the napari viewer\r\n    viewer.window.add_dock_widget(gui)\r\n\r\n    # keep the dropdown menus in the gui in sync with the layer model\r\n    viewer.layers.events.changed.connect(lambda x: gui.refresh_choices())\r\n\r\n    gui.refresh_choices()\r\n\r\n    # load data\r\n    viewer.add_image(example_image)\r\n    viewer.add_labels(example_labels)\r\n```\r\n\r\n## Full error message\r\n```\r\nSegmenting...\r\nWARNING: Traceback (most recent call last):\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/magicgui-0.1.5-py3.8.egg/magicgui/core.py\", line 199, in \u003clambda\u003e\r\n    self.call_button.clicked.connect(lambda checked: self.__call__())\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/magicgui-0.1.5-py3.8.egg/magicgui/core.py\", line 526, in __call__\r\n    value = self.func(**_kwargs)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/segmentify-0.1.1-py3.8.egg/segmentify/gui.py\", line 29, in segmentation\r\n    clf, features = fit(data, initial_labels.data, featurizer=featurizer.value)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/segmentify-0.1.1-py3.8.egg/segmentify/semantic/main.py\", line 129, in fit\r\n    padded_features = unet_featurize(padded_image, featurizer)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/segmentify-0.1.1-py3.8.egg/segmentify/semantic/main.py\", line 59, in unet_featurize\r\n    features = model(image)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/torch-1.5.1-py3.8-linux-x86_64.egg/torch/nn/modules/module.py\", line 550, in __call__\r\n    result = self.forward(*input, **kwargs)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/segmentify-0.1.1-py3.8.egg/segmentify/model/unet.py\", line 57, in forward\r\n    x = self.decode_4(x, skip_4)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/torch-1.5.1-py3.8-linux-x86_64.egg/torch/nn/modules/module.py\", line 550, in __call__\r\n    result = self.forward(*input, **kwargs)\r\n  File \"/home/hungyiwu/.venv/segmentify/lib/python3.8/site-packages/segmentify-0.1.1-py3.8.egg/segmentify/model/layers/unet_layers.py\", line 63, in forward\r\n    output += skip\r\nRuntimeError: The size of tensor a (62) must match the size of tensor b (63) at non-singleton dimension 3\r\nAborted (core dumped)\r\n```\r\n\r\n## Environment, version, and other information\r\npython 3.8.2\r\nnapari 0.3.5\r\nnapari-plugin-engine 0.1.6\r\nnapari-svg 0.1.3\r\nsegmentify 0.1.1 (installed by cloning this repo and `python setup.py install` the `master` branch)\r\nUbuntu 20.04\r\npython venv\r\n`pip freeze \u003e `[requirements.txt](https://github.com/transformify-plugins/segmentify/files/4837652/requirements.txt)\r\n","author":{"url":"https://github.com/hungyiwu","@type":"Person","name":"hungyiwu"},"datePublished":"2020-06-26T15:07:55.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":3},"url":"https://github.com/34/segmentify/issues/34"}