diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..33dd462 --- /dev/null +++ b/.gitignore @@ -0,0 +1,12 @@ +*.py[co] +__pycache__/ + +# build +/niftypet/ml/_dist_ver.py +/build/ +/dist/ +/*.egg*/ + +/.coverage* +/coverage.xml +/.pytest_cache/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..37a25c7 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,45 @@ +default_language_version: + python: python3 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.4.0 + hooks: + - id: check-added-large-files + - id: check-case-conflict + - id: check-docstring-first + - id: check-executables-have-shebangs + - id: check-toml + - id: check-merge-conflict + - id: check-yaml + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + - id: sort-simple-yaml + - id: trailing-whitespace +- repo: local + hooks: + - id: todo + name: Check TODO + language: pygrep + entry: TODO + types: [text] + exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$ + args: [-i] +- repo: https://gitlab.com/pycqa/flake8 + rev: 3.8.4 + hooks: + - id: flake8 + additional_dependencies: + - flake8-bugbear + - flake8-comprehensions + - flake8-debugger + - flake8-string-format +- repo: https://github.com/google/yapf + rev: 6db9374 + hooks: + - id: yapf + args: [-i] +- repo: https://github.com/PyCQA/isort + rev: 5.7.0 + hooks: + - id: isort diff --git a/LICENCE b/LICENCE new file mode 100644 index 0000000..bc8942f --- /dev/null +++ b/LICENCE @@ -0,0 +1,367 @@ +Mozilla Public License Version 2.0 +================================== + +1. Definitions +-------------- + +1.1. "Contributor" + means each individual or legal entity that creates, contributes to + the creation of, or owns Covered Software. + +1.2. "Contributor Version" + means the combination of the Contributions of others (if any) used + by a Contributor and that particular Contributor's Contribution. + +1.3. "Contribution" + means Covered Software of a particular Contributor. + +1.4. "Covered Software" + means Source Code Form to which the initial Contributor has attached + the notice in Exhibit A, the Executable Form of such Source Code + Form, and Modifications of such Source Code Form, in each case + including portions thereof. + +1.5. "Incompatible With Secondary Licenses" + means + + (a) that the initial Contributor has attached the notice described + in Exhibit B to the Covered Software; or + + (b) that the Covered Software was made available under the terms of + version 1.1 or earlier of the License, but not also under the + terms of a Secondary License. + +1.6. "Executable Form" + means any form of the work other than Source Code Form. + +1.7. "Larger Work" + means a work that combines Covered Software with other material, in + a separate file or files, that is not Covered Software. + +1.8. "License" + means this document. + +1.9. "Licensable" + means having the right to grant, to the maximum extent possible, + whether at the time of the initial grant or subsequently, any and + all of the rights conveyed by this License. + +1.10. "Modifications" + means any of the following: + + (a) any file in Source Code Form that results from an addition to, + deletion from, or modification of the contents of Covered + Software; or + + (b) any new file in Source Code Form that contains any Covered + Software. + +1.11. "Patent Claims" of a Contributor + means any patent claim(s), including without limitation, method, + process, and apparatus claims, in any patent Licensable by such + Contributor that would be infringed, but for the grant of the + License, by the making, using, selling, offering for sale, having + made, import, or transfer of either its Contributions or its + Contributor Version. + +1.12. "Secondary License" + means either the GNU General Public License, Version 2.0, the GNU + Lesser General Public License, Version 2.1, the GNU Affero General + Public License, Version 3.0, or any later versions of those + licenses. + +1.13. "Source Code Form" + means the form of the work preferred for making modifications. + +1.14. "You" (or "Your") + means an individual or a legal entity exercising rights under this + License. For legal entities, "You" includes any entity that + controls, is controlled by, or is under common control with You. For + purposes of this definition, "control" means (a) the power, direct + or indirect, to cause the direction or management of such entity, + whether by contract or otherwise, or (b) ownership of more than + fifty percent (50%) of the outstanding shares or beneficial + ownership of such entity. + +2. License Grants and Conditions +-------------------------------- + +2.1. Grants + +Each Contributor hereby grants You a world-wide, royalty-free, +non-exclusive license: + +(a) under intellectual property rights (other than patent or trademark) + Licensable by such Contributor to use, reproduce, make available, + modify, display, perform, distribute, and otherwise exploit its + Contributions, either on an unmodified basis, with Modifications, or + as part of a Larger Work; and + +(b) under Patent Claims of such Contributor to make, use, sell, offer + for sale, have made, import, and otherwise transfer either its + Contributions or its Contributor Version. + +2.2. Effective Date + +The licenses granted in Section 2.1 with respect to any Contribution +become effective for each Contribution on the date the Contributor first +distributes such Contribution. + +2.3. Limitations on Grant Scope + +The licenses granted in this Section 2 are the only rights granted under +this License. No additional rights or licenses will be implied from the +distribution or licensing of Covered Software under this License. +Notwithstanding Section 2.1(b) above, no patent license is granted by a +Contributor: + +(a) for any code that a Contributor has removed from Covered Software; + or + +(b) for infringements caused by: (i) Your and any other third party's + modifications of Covered Software, or (ii) the combination of its + Contributions with other software (except as part of its Contributor + Version); or + +(c) under Patent Claims infringed by Covered Software in the absence of + its Contributions. + +This License does not grant any rights in the trademarks, service marks, +or logos of any Contributor (except as may be necessary to comply with +the notice requirements in Section 3.4). + +2.4. Subsequent Licenses + +No Contributor makes additional grants as a result of Your choice to +distribute the Covered Software under a subsequent version of this +License (see Section 10.2) or under the terms of a Secondary License (if +permitted under the terms of Section 3.3). + +2.5. Representation + +Each Contributor represents that the Contributor believes its +Contributions are its original creation(s) or it has sufficient rights +to grant the rights to its Contributions conveyed by this License. + +2.6. Fair Use + +This License is not intended to limit any rights You have under +applicable copyright doctrines of fair use, fair dealing, or other +equivalents. + +2.7. Conditions + +Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted +in Section 2.1. + +3. Responsibilities +------------------- + +3.1. Distribution of Source Form + +All distribution of Covered Software in Source Code Form, including any +Modifications that You create or to which You contribute, must be under +the terms of this License. You must inform recipients that the Source +Code Form of the Covered Software is governed by the terms of this +License, and how they can obtain a copy of this License. You may not +attempt to alter or restrict the recipients' rights in the Source Code +Form. + +3.2. Distribution of Executable Form + +If You distribute Covered Software in Executable Form then: + +(a) such Covered Software must also be made available in Source Code + Form, as described in Section 3.1, and You must inform recipients of + the Executable Form how they can obtain a copy of such Source Code + Form by reasonable means in a timely manner, at a charge no more + than the cost of distribution to the recipient; and + +(b) You may distribute such Executable Form under the terms of this + License, or sublicense it under different terms, provided that the + license for the Executable Form does not attempt to limit or alter + the recipients' rights in the Source Code Form under this License. + +3.3. Distribution of a Larger Work + +You may create and distribute a Larger Work under terms of Your choice, +provided that You also comply with the requirements of this License for +the Covered Software. If the Larger Work is a combination of Covered +Software with a work governed by one or more Secondary Licenses, and the +Covered Software is not Incompatible With Secondary Licenses, this +License permits You to additionally distribute such Covered Software +under the terms of such Secondary License(s), so that the recipient of +the Larger Work may, at their option, further distribute the Covered +Software under the terms of either this License or such Secondary +License(s). + +3.4. Notices + +You may not remove or alter the substance of any license notices +(including copyright notices, patent notices, disclaimers of warranty, +or limitations of liability) contained within the Source Code Form of +the Covered Software, except that You may alter any license notices to +the extent required to remedy known factual inaccuracies. + +3.5. Application of Additional Terms + +You may choose to offer, and to charge a fee for, warranty, support, +indemnity or liability obligations to one or more recipients of Covered +Software. However, You may do so only on Your own behalf, and not on +behalf of any Contributor. You must make it absolutely clear that any +such warranty, support, indemnity, or liability obligation is offered by +You alone, and You hereby agree to indemnify every Contributor for any +liability incurred by such Contributor as a result of warranty, support, +indemnity or liability terms You offer. You may include additional +disclaimers of warranty and limitations of liability specific to any +jurisdiction. + +4. Inability to Comply Due to Statute or Regulation +--------------------------------------------------- + +If it is impossible for You to comply with any of the terms of this +License with respect to some or all of the Covered Software due to +statute, judicial order, or regulation then You must: (a) comply with +the terms of this License to the maximum extent possible; and (b) +describe the limitations and the code they affect. Such description must +be placed in a text file included with all distributions of the Covered +Software under this License. Except to the extent prohibited by statute +or regulation, such description must be sufficiently detailed for a +recipient of ordinary skill to be able to understand it. + +5. Termination +-------------- + +5.1. The rights granted under this License will terminate automatically +if You fail to comply with any of its terms. However, if You become +compliant, then the rights granted under this License from a particular +Contributor are reinstated (a) provisionally, unless and until such +Contributor explicitly and finally terminates Your grants, and (b) on an +ongoing basis, if such Contributor fails to notify You of the +non-compliance by some reasonable means prior to 60 days after You have +come back into compliance. Moreover, Your grants from a particular +Contributor are reinstated on an ongoing basis if such Contributor +notifies You of the non-compliance by some reasonable means, this is the +first time You have received notice of non-compliance with this License +from such Contributor, and You become compliant prior to 30 days after +Your receipt of the notice. + +5.2. If You initiate litigation against any entity by asserting a patent +infringement claim (excluding declaratory judgment actions, +counter-claims, and cross-claims) alleging that a Contributor Version +directly or indirectly infringes any patent, then the rights granted to +You by any and all Contributors for the Covered Software under Section +2.1 of this License shall terminate. + +5.3. In the event of termination under Sections 5.1 or 5.2 above, all +end user license agreements (excluding distributors and resellers) which +have been validly granted by You or Your distributors under this License +prior to termination shall survive termination. + +************************************************************************ +* * +* 6. Disclaimer of Warranty * +* ------------------------- * +* * +* Covered Software is provided under this License on an "as is" * +* basis, without warranty of any kind, either expressed, implied, or * +* statutory, including, without limitation, warranties that the * +* Covered Software is free of defects, merchantable, fit for a * +* particular purpose or non-infringing. The entire risk as to the * +* quality and performance of the Covered Software is with You. * +* Should any Covered Software prove defective in any respect, You * +* (not any Contributor) assume the cost of any necessary servicing, * +* repair, or correction. This disclaimer of warranty constitutes an * +* essential part of this License. No use of any Covered Software is * +* authorized under this License except under this disclaimer. * +* * +************************************************************************ + +************************************************************************ +* * +* 7. Limitation of Liability * +* -------------------------- * +* * +* Under no circumstances and under no legal theory, whether tort * +* (including negligence), contract, or otherwise, shall any * +* Contributor, or anyone who distributes Covered Software as * +* permitted above, be liable to You for any direct, indirect, * +* special, incidental, or consequential damages of any character * +* including, without limitation, damages for lost profits, loss of * +* goodwill, work stoppage, computer failure or malfunction, or any * +* and all other commercial damages or losses, even if such party * +* shall have been informed of the possibility of such damages. This * +* limitation of liability shall not apply to liability for death or * +* personal injury resulting from such party's negligence to the * +* extent applicable law prohibits such limitation. Some * +* jurisdictions do not allow the exclusion or limitation of * +* incidental or consequential damages, so this exclusion and * +* limitation may not apply to You. * +* * +************************************************************************ + +8. Litigation +------------- + +Any litigation relating to this License may be brought only in the +courts of a jurisdiction where the defendant maintains its principal +place of business and such litigation shall be governed by laws of that +jurisdiction, without reference to its conflict-of-law provisions. +Nothing in this Section shall prevent a party's ability to bring +cross-claims or counter-claims. + +9. Miscellaneous +---------------- + +This License represents the complete agreement concerning the subject +matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed only to the extent +necessary to make it enforceable. Any law or regulation which provides +that the language of a contract shall be construed against the drafter +shall not be used to construe this License against a Contributor. + +10. Versions of the License +--------------------------- + +10.1. New Versions + +Mozilla Foundation is the license steward. Except as provided in Section +10.3, no one other than the license steward has the right to modify or +publish new versions of this License. Each version will be given a +distinguishing version number. + +10.2. Effect of New Versions + +You may distribute the Covered Software under the terms of the version +of the License under which You originally received the Covered Software, +or under the terms of any subsequent version published by the license +steward. + +10.3. Modified Versions + +If you create software not governed by this License, and you want to +create a new license for such software, you may create and use a +modified version of this License if you rename the license and remove +any references to the name of the license steward (except to note that +such modified license differs from this License). + +10.4. Distributing Source Code Form that is Incompatible With Secondary +Licenses + +If You choose to distribute Source Code Form that is Incompatible With +Secondary Licenses under the terms of this version of the License, the +notice described in Exhibit B of this License must be attached. + +Exhibit A - Source Code Form License Notice +------------------------------------------- + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at http://mozilla.org/MPL/2.0/. + +If it is not possible or desirable to put the notice in a particular +file, then You may include the notice in a location (such as a LICENSE +file in a relevant directory) where a recipient would be likely to look +for such a notice. + +You may add additional accurate notices of copyright ownership. diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..704807d --- /dev/null +++ b/README.rst @@ -0,0 +1,21 @@ +PET-MR Machine Learning +======================= + +|Version| |Py-Versions| |Licence| |Tests| + + +Licence +~~~~~~~ + +|Licence| + +Copyright 2021 + +.. |Licence| image:: https://img.shields.io/pypi/l/niftyml.svg?label=licence + :target: https://github.com/NiftyPET/niftyml/blob/master/LICENCE +.. |Tests| image:: https://img.shields.io/github/workflow/status/NiftyPET/niftyml/Test?logo=GitHub + :target: https://github.com/NiftyPET/niftyml/actions +.. |Version| image:: https://img.shields.io/pypi/v/niftyml.svg?logo=python&logoColor=white + :target: https://github.com/NiftyPET/niftyml/releases +.. |Py-Versions| image:: https://img.shields.io/pypi/pyversions/niftyml.svg?logo=python&logoColor=white + :target: https://pypi.org/project/niftyml diff --git a/niftypet/__init__.py b/niftypet/__init__.py new file mode 100644 index 0000000..8db66d3 --- /dev/null +++ b/niftypet/__init__.py @@ -0,0 +1 @@ +__path__ = __import__("pkgutil").extend_path(__path__, __name__) diff --git a/niftypet/ml/__init__.py b/niftypet/ml/__init__.py new file mode 100644 index 0000000..6aa4af7 --- /dev/null +++ b/niftypet/ml/__init__.py @@ -0,0 +1,18 @@ +""" +Neuro-image Machine Learning. +""" +__author__ = "Casper da Costa-Luis <imaging@cdcl.ml>" +__date__ = "2021" +# version detector. Precedence: installed dist, git, 'UNKNOWN' +try: + from ._dist_ver import __version__ +except ImportError: + try: + from setuptools_scm import get_version + + __version__ = get_version(root="../..", relative_to=__file__) + except (ImportError, LookupError): + __version__ = "UNKNOWN" + +from .layers import * # NOQA, yapf: disable +from .models import * # NOQA, yapf: disable diff --git a/niftypet/ml/layers.py b/niftypet/ml/layers.py new file mode 100644 index 0000000..06e80eb --- /dev/null +++ b/niftypet/ml/layers.py @@ -0,0 +1,135 @@ +import logging +from collections import Iterable + +from tensorflow import keras +from tensorflow import math as tfm + +log = logging.getLogger(__name__) + + +def nrmse(y_true, y_pred): + return tfm.sqrt( + tfm.reduce_mean(tfm.squared_difference(y_true, y_pred)) / tfm.reduce_mean(y_true**2)) + + +class Norm(keras.layers.Layer): + """per-channel mean and std normalisation""" + def __init__(self, mean=False, std=True, eps=1e-6, batch=False, **kwargs): + self.mean = mean + self.std = std + self.eps = eps + self.batch = batch + super(Norm, self).__init__(**kwargs) + + def get_config(self): + config = super(Norm, self).get_config().copy() + config.update(mean=self.mean) + config.update(std=self.std) + config.update(eps=self.eps) + config.update(batch=self.batch) + return config + + def compute_output_shape(self, input_shape): + return input_shape + + def call(self, x): + input_shape = x.shape.as_list() + axis = tuple(range(0 if self.batch else 1, len(input_shape) if input_shape else 4)) + if self.mean: + x = x - tfm.reduce_mean(x, axis=axis, keepdims=True) + if self.std: + std = tfm.sqrt(tfm.reduce_mean(tfm.square(x), axis=axis, keepdims=True)) + elif self.std: + std = tfm.reduce_std(x, axis=axis, keepdims=True) + return x / ((self.eps + std) if self.eps else std) if self.std else x + + +class LocalityAdaptive(keras.layers.Layer): + """ + Locality Adaptive[1]: per-ROI convolution. + + >>> x = keras.backend.variable(np.arange(3*64*32*2).reshape(3,64,32,2)) + >>> lALayer = LocalityAdaptive(roi_size=32) + >>> out = lALayer(x) + >>> lALayer.set_weights([np.array([[0.5, 0.5], [0.9, 0.1]])[:, None, :, None]]) + >>> out = lALayer(x) + >>> assert out.shape[:-1] == x.shape[:-1] + >>> assert keras.backend.all(sum(x[0, 1, 1] * [0.5, 0.5]) - out[0, 1, 1] < 1e-6) + >>> assert keras.backend.all(sum(x[0, -1, -1] * [0.9, 0.1]) - out[0, -1, -1] < 1e-6) + + [1] Wang et al. 2019 TMI 38(6) 1328-1339 + "3D Auto-Context-Based Locality Adaptive Multi-Modality GANs for PET Synthesis" + """ + def __init__(self, filters=1, roi_size=32, **kwargs): + assert filters == 1, NotImplementedError + self.filters = filters + self.roi_size = roi_size + super(LocalityAdaptive, self).__init__(**kwargs) + # assert self.data_format and self.data_format != "channels_first" + + def get_config(self): + config = super(LocalityAdaptive, self).get_config().copy() + config.update(filters=self.filters) + config.update(roi_size=self.roi_size) + return config + + def build(self, input_shape): + in_dims = input_shape[1:-1] + roi = self.roi_size + if not isinstance(roi, Iterable): + roi = (roi,) * len(in_dims) + + in_ch = input_shape[-1] + self.kernel = self.add_weight( + name="kernel", + shape=tuple((i+j-1) // j for i, j in zip(in_dims, roi)) + (in_ch, self.filters), + initializer=keras.initializers.constant(1.0 / in_ch), + trainable=True, + ) + super(LocalityAdaptive, self).build(input_shape) + + @staticmethod + def _call_helper(x, knl, roi, axis=0): + """ + Recursive helper using concatenation. + Required since tensors cannot be assinged to. + + x : shape [N, x0, ..., xn-1, C] + knl : shape [s0, ..., sn-1, C, filters]: weights + Note that there are `s0*...*sn` patches, + each with its own kernel of shape [1, C, filters] + roi : shape [r0, ..., rn-1]: patch shape + axis : in range(n), which axis to expand/concatenate over + """ + assert axis >= 0 + # s0, ..., sn-1, C, filters + shp_knl = knl.shape.as_list() + padding = (slice(0, None),) * axis + log.debug("knl.shape:{}, axis:{}".format(shp_knl, axis)) + KB = keras.backend + if axis == len(shp_knl) - 3: + conv = {3: KB.conv1d, 4: KB.conv2d, 5: KB.conv3d}[len(shp_knl)] + out = [ + conv( + x[(slice(0, None),) + padding + (slice(i * roi[axis], (i+1) * roi[axis]),)], + knl[padding + (slice(i, i + 1),)], + ) for i in range(shp_knl[axis])] + else: + out = [ + LocalityAdaptive._call_helper( + x[(slice(0, None),) + padding + (slice(i * roi[axis], (i+1) * roi[axis]),)], + knl[padding + (slice(i, i + 1),)], + roi, + axis=axis + 1, + ) for i in range(shp_knl[axis])] + return KB.concatenate(out, axis=1 + axis) + + def call(self, x): + in_dims = x.shape.as_list()[1:-1] + roi = self.roi_size + if not isinstance(roi, Iterable): + roi = (roi,) * len(in_dims) + return self._call_helper(x, self.kernel, roi) + + def compute_output_shape(self, input_shape): + return input_shape[:-1] + (self.filters,) diff --git a/niftypet/ml/models.py b/niftypet/ml/models.py new file mode 100644 index 0000000..c2d790a --- /dev/null +++ b/niftypet/ml/models.py @@ -0,0 +1,117 @@ +""" +PET-MR denoising CNNs. +""" +import functools +import logging + +from tensorflow import keras + +from .layers import Norm as NormLayer +from .layers import nrmse + +__author__ = "Casper da Costa-Luis <imaging@cdcl.ml>" +log = logging.getLogger(__name__) +L = keras.layers +CONV_ND = {2: L.Conv1D, 3: L.Conv2D, 4: L.Conv3D} +MAXPOOL_ND = {2: L.MaxPool1D, 3: L.MaxPool2D, 4: L.MaxPool3D} +UPSAMPLE_ND = {2: L.UpSampling1D, 3: L.UpSampling2D, 4: L.UpSampling3D} + + +def dcl2020(input_shape, n_filters=None, filter_sizes=None, activations=None, prenorm=None, eps=0, + lr=1e-3, dtype="float32"): + """ + Micro-net implementation based on: + C. O. da Costa-Luis and A. J. Reader 2021 IEEE Trans. Radiat. Plasma Med. Sci. 5(2) 202-212 + "Micro-Networks for Robust MR-Guided Low Count PET Imaging" + + Args: + n_filters: default [32, 32, 1] + filter_sizes: default [5, 3, 1] + activations: default ['sigmoid', ..., 'sigmoid', 'elu'] + prenorm: default is `activation[-1] != 'sigmoid'` + wd: weigth for discriminator loss term + """ + n_filters = n_filters or [32, 32, 1] + filter_sizes = filter_sizes or [5, 3, 1] + activations = activations or ["sigmoid"] * (len(n_filters) - 1) + ["elu"] + + Conv = CONV_ND[len(input_shape)] + + x = inputs = L.Input(input_shape, dtype=dtype) + + largs = { + 'kernel_initializer': "he_normal", 'bias_initializer': "he_normal", 'padding': "same", + 'strides': 1} + Norm = functools.partial(NormLayer, eps=eps, std=True, batch=True) + + inputs = x = L.Input(input_shape, dtype=dtype) + if prenorm is None: + prenorm = activations[-1] != 'sigmoid' + if prenorm: + x = L.concatenate([Norm(mean=True)(x[..., :1]), Norm(mean=False)(x[..., 1:])]) # MR # PET + + for filters, kernel_size, activation in zip(n_filters, filter_sizes, activations): + x = Conv(filters, kernel_size, activation=activation, **largs)(x) + # x = L.Multiply()((x, std)) # un-norm + + model = keras.Model(inputs=inputs, outputs=x) + if lr: + opt = keras.optimizers.Adam(lr) + model.compile(opt, metrics=[nrmse], loss=nrmse) + model.summary(print_fn=log.debug) + return model + + +def chen2019(input_shape, residual_input_channel=1, lr=2e-4, dtype="float32"): + """ + Residual U-net implementation based on: + K. T. Chen et al. 2019 Radiol. 290(3) 649-656 + "Ultra-Low-Dose 18F-Florbetaben Amyloid PET Imaging Using Deep Learning + with Multi-Contrast MRI Inputs" + + >>> model = network(input_data.shape[1:]) + >>> model.fit(input_data, output_date, epochs=100, batch_size=input_data.shape[0] // 4, ...) + + Args: + input_shape (tuple): (num_slices, slice_height, slice_width, num_channels) + residual_input_channel : input channel index to use for residual addition + """ + Conv = CONV_ND[len(input_shape)] + MaxPool = MAXPOOL_ND[len(input_shape)] + Upsample = UPSAMPLE_ND[len(input_shape)] + + x = inputs = L.Input(input_shape, dtype=dtype) + + def block(x, filters): + x = Conv(filters, 3, padding="same", use_bias=False, dtype=dtype)(x) + x = L.BatchNormalization(dtype=dtype)(x) + x = L.ReLU(dtype=dtype)(x) + return x + + # U-net + filters = [16, 32, 64, 128] + # # encode + convs = [] + for i in filters[:-1]: + x = block(x, i) + x = block(x, i) + convs.append(x) + x = MaxPool(dtype=dtype, padding="same")(x) + x = block(x, filters[-1]) + x = block(x, filters[-1]) + # # decode + for i in filters[:-1][::-1]: + x = Upsample(interpolation="bilinear", dtype=dtype)(x) + x = L.Concatenate()([x, convs.pop()]) + x = block(x, i) + x = block(x, i) + x = Conv(1, 1, padding="same", dtype=dtype, name="residual")(x) + x = L.Add(name="generated")([ + inputs[..., residual_input_channel:residual_input_channel + 1], x]) + + model = keras.Model(inputs=inputs, outputs=x) + if lr: + opt = keras.optimizers.Adam(lr) + model.compile(opt, metrics=[nrmse], loss="mae") + model.summary(print_fn=log.debug) + return model diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..4eb7149 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,6 @@ +[build-system] +requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"] + +[tool.setuptools_scm] +write_to = "niftypet/ml/_dist_ver.py" +write_to_template = "__version__ = '{version}'\n" diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..89e3eb1 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,80 @@ +[metadata] +name=niftyml +description=PET-MR Machine Learning +long_description=file: README.rst +long_description_content_type=text/x-rst +license=MPL 2.0 +license_file=LICENCE +url=https://github.com/NiftyPET/niftyml +project_urls= + Changelog=https://github.com/NiftyPET/niftyml/releases +author=Casper da Costa-Luis +author_email=imaging@cdcl.ml +keywords=PET, ML +provides=niftypet.ml +classifiers= + Development Status :: 4 - Beta + Intended Audience :: Developers + Intended Audience :: Education + Intended Audience :: Science/Research + License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0) + Operating System :: MacOS + Operating System :: Microsoft :: Windows + Operating System :: POSIX :: Linux + Operating System :: Unix + Programming Language :: Python + Programming Language :: Python :: 3 + Programming Language :: Python :: 3.6 + Programming Language :: Python :: 3.7 + Programming Language :: Python :: 3.8 + Programming Language :: Python :: 3.9 + Topic :: Software Development :: Libraries + Topic :: Software Development :: Libraries :: Python Modules +[options] +python_requires=>=3.6 +install_requires=numpy +packages=find: +[options.extras_require] +dev= + pre-commit + pytest + pytest-cov + pytest-timeout + codecov +[options.packages.find] +exclude=tests + +[yapf] +spaces_before_comment=15, 20 +arithmetic_precedence_indication=true +allow_split_before_dict_value=false +coalesce_brackets=True +column_limit=99 +each_dict_entry_on_separate_line=False +space_between_ending_comma_and_closing_bracket=False +split_before_named_assigns=False +split_before_closing_bracket=False + +[isort] +profile=black +line_length=99 +known_first_party=niftypet,tests + +[flake8] +statistics=True +max_line_length=99 +extend-ignore=E261,P101 +exclude=.git,__pycache__,build,dist,.eggs + +[tool:pytest] +timeout=30 +log_level=INFO +python_files=tests/test_*.py +addopts=-v --tb=short -rxs -W=error --durations=0 --durations-min=1 --cov=niftypet.ml --cov-report=term-missing --cov-report=xml + +[coverage:run] +branch=True +include=niftypet/ml/* +relative_files=True +[coverage:report] +show_missing=True diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..d5d43d7 --- /dev/null +++ b/setup.py @@ -0,0 +1,3 @@ +from setuptools import setup + +setup(use_scm_version=True) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29