Tiling #160
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Tiling #160
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| preprocess = [ | ||
| {"spec": "ij.IJ::runMacroFile", | ||
| "kwargs": macro} | ||
| ] |
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| preprocess = [ | |
| {"spec": "ij.IJ::runMacroFile", | |
| "kwargs": macro} | |
| ] | |
| preprocess = [{"spec": "ij.IJ::runMacroFile", "kwargs": macro}] |
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| def _get_deepimagej_config(export_folder, | ||
| sample_inputs, sample_outputs, | ||
| test_in_path, test_out_path, | ||
| preprocessing): |
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| def _get_deepimagej_config(export_folder, | |
| sample_inputs, sample_outputs, | |
| test_in_path, test_out_path, | |
| preprocessing): | |
| def _get_deepimagej_config(export_folder, sample_inputs, sample_outputs, test_in_path, test_out_path, preprocessing): |
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| { | ||
| "name": in_path, | ||
| "size": _get_size(in_path), | ||
| "pixel_size": {"x": 1.0, "y": 1.0, "z": 1.0} | ||
| } for in_path in sample_inputs | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "name": out_path, | ||
| "type": "image", | ||
| "size": _get_size(out_path) | ||
| } for out_path in sample_outputs |
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| { | |
| "name": in_path, | |
| "size": _get_size(in_path), | |
| "pixel_size": {"x": 1.0, "y": 1.0, "z": 1.0} | |
| } for in_path in sample_inputs | |
| ], | |
| "outputs": [ | |
| { | |
| "name": out_path, | |
| "type": "image", | |
| "size": _get_size(out_path) | |
| } for out_path in sample_outputs | |
| {"name": in_path, "size": _get_size(in_path), "pixel_size": {"x": 1.0, "y": 1.0, "z": 1.0}} | |
| for in_path in sample_inputs |
| "size": _get_size(out_path) | ||
| } for out_path in sample_outputs | ||
| ], | ||
| "memory_peak": None, |
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| "memory_peak": None, | |
| "outputs": [{"name": out_path, "type": "image", "size": _get_size(out_path)} for out_path in sample_outputs], | |
| "memory_peak": None, |
| } for out_path in sample_outputs | ||
| ], | ||
| "memory_peak": None, | ||
| "runtime": None |
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| "runtime": None | |
| "runtime": None, |
| # other stuff deepimagej needs | ||
| "pyramidal_model": False, | ||
| "allow_tiling": True, | ||
| "model_keys": None |
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| "model_keys": None | |
| "model_keys": None, |
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| sample_in_path, sample_out_path = _write_sample_data(test_inputs, | ||
| test_outputs, | ||
| root) | ||
| ij_config, attachments = _get_deepimagej_config(root, | ||
| sample_in_path, sample_out_path, | ||
| test_inputs, test_outputs, | ||
| preprocessing) |
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| sample_in_path, sample_out_path = _write_sample_data(test_inputs, | |
| test_outputs, | |
| root) | |
| ij_config, attachments = _get_deepimagej_config(root, | |
| sample_in_path, sample_out_path, | |
| test_inputs, test_outputs, | |
| preprocessing) | |
| sample_in_path, sample_out_path = _write_sample_data(test_inputs, test_outputs, root) | |
| ij_config, attachments = _get_deepimagej_config( | |
| root, sample_in_path, sample_out_path, test_inputs, test_outputs, preprocessing | |
| ) |
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| kwargs.update({ | ||
| "sample_inputs": [sample_in_path], | ||
| "sample_outputs": [sample_out_path], | ||
| "config": config | ||
| }) |
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| kwargs.update({ | |
| "sample_inputs": [sample_in_path], | |
| "sample_outputs": [sample_out_path], | |
| "config": config | |
| }) | |
| kwargs.update({"sample_inputs": [sample_in_path], "sample_outputs": [sample_out_path], "config": config}) |
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| spec_path, | ||
| out_path, | ||
| weight_type, | ||
| tensorflow_version=None, | ||
| use_implicit_output_shape=False, | ||
| for_deepimagej=True |
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| spec_path, | |
| out_path, | |
| weight_type, | |
| tensorflow_version=None, | |
| use_implicit_output_shape=False, | |
| for_deepimagej=True | |
| spec_path, out_path, weight_type, tensorflow_version=None, use_implicit_output_shape=False, for_deepimagej=True |
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| predict_image( | ||
| any_model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"} | ||
| model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"} | ||
| ) |
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| predict_image( | |
| any_model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"} | |
| model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"} | |
| ) | |
| predict_image(model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"}) |
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Fixes #157.
Pending #159 and bioimage-io/spec-bioimage-io#282.