Merge 5b9c035 into 39fab86

.github/workflows/docker-image.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      TF_VERSION: 1.14.0
+      TF_VERSION: 2.3.1
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/tests.yaml

@@ -13,8 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [2.7, 3.6, 3.7]
-        tensorflow-version: [1.14.0, 1.15.0]
+        python-version: [3.5, 3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -38,15 +37,13 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        sed -i "/tensorflow/d" requirements.txt
-        pip install tensorflow==${{ matrix.tensorflow-version }}
         pip install -r requirements.txt
         pip install -r requirements-test.txt
 
     - name: Run PyTest and Coveralls
       env:
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        COVERALLS_FLAG_NAME: py${{ matrix.python-version }}-tf${{ matrix.tensorflow-version }}
+        COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
         COVERALLS_PARALLEL: true
       run: |
         pytest --cov deepcell --pep8

Dockerfile

@@ -1,40 +1,32 @@
 # Use tensorflow/tensorflow as the base image
 # Change the build arg to edit the tensorflow version.
 # Only supporting python3.
-ARG TF_VERSION=1.14.0-gpu
+ARG TF_VERSION=2.3.1-gpu
 
-FROM tensorflow/tensorflow:${TF_VERSION}-py3
+FROM tensorflow/tensorflow:${TF_VERSION}
 
 # System maintenance
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-    python3-tk \
+    libxext6 \
+    libxrender-dev \
     libsm6 && \
     rm -rf /var/lib/apt/lists/* && \
-    /usr/local/bin/pip install --upgrade pip
+    /usr/bin/python3 -m pip install --upgrade pip
 
 WORKDIR /notebooks
 
 # Copy the setup.py and requirements.txt and install the deepcell-tf dependencies
 COPY setup.py requirements.txt /opt/deepcell-tf/
 
 # Prevent reinstallation of tensorflow and install all other requirements.
-RUN sed -i "/tensorflow/d" /opt/deepcell-tf/requirements.txt && \
+RUN sed -i "/tensorflow>/d" /opt/deepcell-tf/requirements.txt && \
     pip install -r /opt/deepcell-tf/requirements.txt
 
 # Copy the rest of the package code and its scripts
 COPY deepcell /opt/deepcell-tf/deepcell
 
 # Install deepcell via setup.py
-RUN pip install /opt/deepcell-tf && \
-    cd /opt/deepcell-tf && \
-    python setup.py build_ext --inplace
-
-# Older versions of TensorFlow have notebooks, but they may not exist
-RUN if [ -n "$(find /notebooks/ -prune)" ] ; then \
-      mkdir -p /notebooks/intro_to_tensorflow && \
-      ls -d /notebooks/* | grep -v intro_to_tensorflow | \
-      xargs -r mv -t /notebooks/intro_to_tensorflow ; \
-    fi
+RUN pip install /opt/deepcell-tf
 
 # Copy over deepcell notebooks
 COPY notebooks/ /notebooks/

README.md

@@ -75,7 +75,7 @@ For examples of how to train models with the `deepcell-tf` library, check out th
 ```bash
 git clone https://github.com/vanvalenlab/deepcell-tf.git
 cd deepcell-tf
-docker build --build-arg TF_VERSION=1.15.0-gpu -t $USER/deepcell-tf .
+docker build --build-arg TF_VERSION=2.3.1-gpu -t $USER/deepcell-tf .
 ```
 
 ### Run the new docker image

deepcell/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/application.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/application_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import numpy as np
 
-from tensorflow.python.keras.layers import Input
+from tensorflow.keras.layers import Input
 from tensorflow.python.platform import test
 
 from deepcell.applications import Application

deepcell/applications/cell_tracking.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -29,7 +29,7 @@
 from __future__ import division
 from __future__ import print_function
 
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow.keras.utils import get_file
 
 import deepcell_tracking
 from deepcell_toolbox.processing import normalize

deepcell/applications/cell_tracking_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/cytoplasm_segmentation.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import os
 
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow.keras.utils import get_file
 
 from deepcell_toolbox.deep_watershed import deep_watershed
 from deepcell_toolbox.processing import phase_preprocess

deepcell/applications/cytoplasm_segmentation_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/label_detection.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -29,8 +29,8 @@
 from __future__ import division
 from __future__ import print_function
 
-from tensorflow.python import keras
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow import keras
+from tensorflow.keras.utils import get_file
 
 from deepcell.layers import ImageNormalization2D, TensorProduct
 from deepcell.utils.backbone_utils import get_backbone

deepcell/applications/label_detection_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import numpy as np
 
-from tensorflow.python.keras.layers import Input
+from tensorflow.keras.layers import Input
 from tensorflow.python.platform import test
 
 from deepcell.applications import LabelDetectionModel

deepcell/applications/multiplex_segmentation.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,9 +31,7 @@
 
 import os
 
-import numpy as np
-
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow.keras.utils import get_file
 
 from deepcell_toolbox.multiplex_utils import \
     multiplex_preprocess, multiplex_postprocess, format_output_multiplex

deepcell/applications/multiplex_segmentation_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/nuclear_segmentation.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import os
 
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow.keras.utils import get_file
 
 from deepcell_toolbox.processing import normalize
 from deepcell_toolbox.deep_watershed import deep_watershed

deepcell/applications/nuclear_segmentation_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/applications/scale_detection.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -29,8 +29,8 @@
 from __future__ import division
 from __future__ import print_function
 
-from tensorflow.python import keras
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow import keras
+from tensorflow.keras.utils import get_file
 
 from deepcell.layers import ImageNormalization2D, TensorProduct
 from deepcell.utils.backbone_utils import get_backbone

deepcell/applications/scale_detection_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import numpy as np
 
-from tensorflow.python.keras.layers import Input
+from tensorflow.keras.layers import Input
 from tensorflow.python.platform import test
 
 from deepcell.applications import ScaleDetectionModel

deepcell/callbacks.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -29,7 +29,7 @@
 from __future__ import print_function
 from __future__ import division
 
-from tensorflow.python.keras.callbacks import Callback
+from tensorflow.keras.callbacks import Callback
 
 from deepcell.utils.retinanet_anchor_utils import evaluate, evaluate_mask
 
@@ -152,13 +152,12 @@ def on_epoch_end(self, epoch, logs=None):
         else:
             mean_ap = sum(precisions) / sum(x > 0 for x in instances)
 
-        if self.tensorboard is not None and self.tensorboard.writer is not None:
+        if self.tensorboard is not None:
             import tensorflow as tf
-            summary = tf.Summary()
-            summary_value = summary.value.add()  # pylint: disable=E1101
-            summary_value.simple_value = mean_ap
-            summary_value.tag = 'mAP'
-            self.tensorboard.writer.add_summary(summary, epoch)
+            writer = tf.summary.create_file_writer(self.tensorboard.log_dir)
+            with writer.as_default():
+                tf.summary.scalar('mAP', mean_ap, step=epoch)
+                writer.flush()
 
         logs['mAP'] = mean_ap
 

deepcell/callbacks_test.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -49,6 +49,7 @@
 BATCH_SIZE = 5
 
 
+@keras_parameterized.run_with_all_model_types
 @keras_parameterized.run_all_keras_modes
 class CallbacksTest(keras_parameterized.TestCase):
 
@@ -61,8 +62,8 @@ def test_RedirectModel(self):
                 input_shape=(INPUT_DIM,),
                 num_classes=NUM_CLASSES)
 
-            y_test = keras.utils.to_categorical(y_test)
-            y_train = keras.utils.to_categorical(y_train)
+            y_test = keras.utils.np_utils.to_categorical(y_test)
+            y_train = keras.utils.np_utils.to_categorical(y_train)
             model = keras.models.Sequential()
             model.add(
                 keras.layers.Dense(

deepcell/datasets/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -31,7 +31,7 @@
 
 import os
 
-from tensorflow.python.keras.utils.data_utils import get_file
+from tensorflow.keras.utils import get_file
 
 from deepcell.utils.data_utils import get_data
 

deepcell/datasets/cytoplasm.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/datasets/phase.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/datasets/tracked.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.

deepcell/image_generators/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.
@@ -37,8 +37,8 @@
 
 import numpy as np
 
-from tensorflow.python.keras import backend as K
-from tensorflow.python.keras.utils import to_categorical
+from tensorflow.keras import backend as K
+from tensorflow.keras.utils import to_categorical
 
 from deepcell.utils import transform_utils
 

deepcell/image_generators/cropping.py

@@ -1,4 +1,4 @@
-# Copyright 2016-2019 The Van Valen Lab at the California Institute of
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
 # Technology (Caltech), with support from the Paul Allen Family Foundation,
 # Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 # All rights reserved.