Merge pull request #114 from BBQuercus/release_0.1

BBQuercus · web-flow · commit b36382bd195d · 2020-12-12T14:19:37.000+01:00
Release 0.1!
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.8
+current_version = 0.1.0
 commit = False
 tag = True
 
diff --git a/README.md b/README.md
@@ -62,7 +62,7 @@ appropriate `CUDA` and `cuDNN` verions matching your [GPU setup](https://docs.nv
 
 
 ## Usage
-Inferencing on deepBlink is performed at the command line as follows:
+A video overview can be found [here](https://www.youtube.com/watch?v=vlXMg4k79LQ). Inferencing on deepBlink is performed at the command line as follows:
 
 ```bash
 deepblink predict -m MODEL -i INPUT [-o OUTPUT] [-r RADIUS] [-s SHAPE]
diff --git a/benchmarks/deepblink/deepblink_test.py b/benchmarks/deepblink/deepblink_test.py
@@ -45,4 +45,3 @@ def delayed_coordinates_pink(mask):
         delayed_coordinates=delayed_coordinates_pink,
     )
     results_deepblink.to_csv("deepblink.csv")
-
diff --git a/benchmarks/detnet/detnet_test.py b/benchmarks/detnet/detnet_test.py
@@ -44,4 +44,3 @@ def model_loader_detnet(fname):
         delayed_coordinates=delayed_coordinates,
     )
     results_detnet.to_csv("detnet.csv")
-
diff --git a/benchmarks/detnet/run.sh b/benchmarks/detnet/run.sh
@@ -1,10 +1,11 @@
 dataset=/tungstenfs/scratch/shared/gchao_ggiorget/datasets/publication
 savedir=/tungstenfs/scratch/shared/gchao_ggiorget/benchmarks/spotlearn
 
-nice -n 19 python detnet_train.py --dataset ${dataset}/fixed.npz --savedir ${savedir}
 nice -n 19 python detnet_train.py --dataset ${dataset}/microtubule.npz --savedir ${savedir}
-nice -n 19 python detnet_train.py --dataset ${dataset}/mrna.npz --savedir ${savedir}
+nice -n 19 python detnet_train.py --dataset ${dataset}/particle.npz --savedir ${savedir}
 nice -n 19 python detnet_train.py --dataset ${dataset}/receptor.npz --savedir ${savedir}
+nice -n 19 python detnet_train.py --dataset ${dataset}/smfish.npz --savedir ${savedir}
+nice -n 19 python detnet_train.py --dataset ${dataset}/suntag.npz --savedir ${savedir}
 nice -n 19 python detnet_train.py --dataset ${dataset}/vesicle.npz --savedir ${savedir}
 
 nice -n 19 python detnet_test.py --datasets ${dataset} --models ${savedir}/best
diff --git a/benchmarks/spotlearn/run.sh b/benchmarks/spotlearn/run.sh
@@ -1,10 +1,11 @@
 dataset=/tungstenfs/scratch/shared/gchao_ggiorget/datasets/publication
 savedir=/tungstenfs/scratch/shared/gchao_ggiorget/benchmarks/spotlearn
 
-# nice -n 19 python spotlearn_train.py --dataset ${dataset}/fixed.npz --savedir ${savedir}
-# nice -n 19 python spotlearn_train.py --dataset ${dataset}/microtubule.npz --savedir ${savedir}
-# nice -n 19 python spotlearn_train.py --dataset ${dataset}/mrna.npz --savedir ${savedir}
-# nice -n 19 python spotlearn_train.py --dataset ${dataset}/receptor.npz --savedir ${savedir}
-# nice -n 19 python spotlearn_train.py --dataset ${dataset}/vesicle.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/microtubule.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/particle.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/receptor.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/smfish.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/suntag.npz --savedir ${savedir}
+nice -n 19 python spotlearn_train.py --dataset ${dataset}/vesicle.npz --savedir ${savedir}
 
 nice -n 19 python spotlearn_test.py --datasets ${dataset} --models ${savedir}/best
diff --git a/benchmarks/trackmate/run.sh b/benchmarks/trackmate/run.sh
@@ -1,32 +1,37 @@
 dataset=/tungstenfs/scratch/shared/gchao_ggiorget/datasets/publication
 basedir=/tungstenfs/scratch/shared/gchao_ggiorget/benchmarks/trackmate
 
-nice -n 19 python trackmate_prepare.py --dataset ${dataset}/fixed.npz --output ${basedir}
 nice -n 19 python trackmate_prepare.py --dataset ${dataset}/microtubule.npz --output ${basedir}
-nice -n 19 python trackmate_prepare.py --dataset ${dataset}/mrna.npz --output ${basedir}
+nice -n 19 python trackmate_prepare.py --dataset ${dataset}/particle.npz --output ${basedir}
 nice -n 19 python trackmate_prepare.py --dataset ${dataset}/receptor.npz --output ${basedir}
+nice -n 19 python trackmate_prepare.py --dataset ${dataset}/smfish.npz --output ${basedir}
+nice -n 19 python trackmate_prepare.py --dataset ${dataset}/suntag.npz --output ${basedir}
 nice -n 19 python trackmate_prepare.py --dataset ${dataset}/vesicle.npz --output ${basedir}
 
-nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/fixed"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/microtubule"'
-nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/mrna"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/particle"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/receptor"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/smfish"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/suntag"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_train_fiji.py 'basedir="${basedir}/vesicle"'
 
-nice -n 19 python trackmate_train.py --basedir ${basedir}/fixed
 nice -n 19 python trackmate_train.py --basedir ${basedir}/microtubule
-nice -n 19 python trackmate_train.py --basedir ${basedir}/mrna
+nice -n 19 python trackmate_train.py --basedir ${basedir}/particle
 nice -n 19 python trackmate_train.py --basedir ${basedir}/receptor
+nice -n 19 python trackmate_train.py --basedir ${basedir}/smfish
+nice -n 19 python trackmate_train.py --basedir ${basedir}/suntag
 nice -n 19 python trackmate_train.py --basedir ${basedir}/vesicle
 
-nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/fixed",detector="log",radius="5.0",median="False"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/microtubule",detector="log",radius="3.0",median="False"'
-nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/mrna",detector="log",radius="3.0",median="False"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/particle",detector="log",radius="3.0",median="False"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/receptor",detector="log",radius="3.0",median="False"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/smfish",detector="log",radius="5.0",median="False"'
+nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/suntag",detector="log",radius="1.0",median="False"'
 nice -n 19 Fiji.app/ImageJ-linux64 --ij2 --headless --run trackmate_test_fiji.py 'basedir="${basedir}/vesicle",detector="log",radius="5.0",median="False"'
 
-nice -n 19 python trackmate_test.py --basedir ${basedir}/fixed --threshold 8.071781
 nice -n 19 python trackmate_test.py --basedir ${basedir}/microtubule --threshold 1.091255
-nice -n 19 python trackmate_test.py --basedir ${basedir}/mrna --threshold 0.021363
+nice -n 19 python trackmate_test.py --basedir ${basedir}/particle --threshold 0.021363
 nice -n 19 python trackmate_test.py --basedir ${basedir}/receptor --threshold 0.794764
+nice -n 19 python trackmate_test.py --basedir ${basedir}/smfish --threshold 8.071781
+nice -n 19 python trackmate_test.py --basedir ${basedir}/suntag --threshold 0.170
 nice -n 19 python trackmate_test.py --basedir ${basedir}/vesicle --threshold 0.0625
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,6 +1,6 @@
 package:
     name: "deepblink"
-    version: 0.0.8
+    version: 0.1.0
 source:
     path: ..
 
diff --git a/deepblink/__init__.py b/deepblink/__init__.py
@@ -16,7 +16,7 @@
 - util: Basic utility functions not fitting into a category.
 """
 
-__version__ = "0.0.8"
+__version__ = "0.1.0"
 
 from . import augment
 from . import cli
diff --git a/deepblink/cli/_parseutil.py b/deepblink/cli/_parseutil.py
@@ -126,7 +126,7 @@ def _add_utils(parser: argparse.ArgumentParser):
         "-V",
         "--version",
         action="version",
-        version="%(prog)s 0.0.8",
+        version="%(prog)s 0.1.0",
         help="Show %(prog)s's version number.",
     )
     group.add_argument(
diff --git a/deepblink/cli/models.txt b/deepblink/cli/models.txt
@@ -1 +1 @@
-{"fixed":"https://ndownloader.figshare.com/files/25460537","vesicle":"https://ndownloader.figshare.com/files/25460540","receptor":"https://ndownloader.figshare.com/files/25460543","mrna":"https://ndownloader.figshare.com/files/25460546","microtubule":"https://ndownloader.figshare.com/files/25460549","live":"https://ndownloader.figshare.com/files/25460552"}
+{"vesicle":"https://ndownloader.figshare.com/files/25460540","receptor":"https://ndownloader.figshare.com/files/25460543","microtubule":"https://ndownloader.figshare.com/files/25460549","particle":"https://ndownloader.figshare.com/files/25737161","smfish":"https://ndownloader.figshare.com/files/25737164","suntag":"https://ndownloader.figshare.com/files/25737167"}
diff --git a/docs/conf.py b/docs/conf.py
@@ -37,7 +37,7 @@
 year = "2020"
 author = "Bastian Eichenberger"
 copyright = f"{year}, {author}"
-version = release = "0.0.8"
+version = release = "0.1.0"
 
 pygments_style = "trac"
 templates_path = ["."]
diff --git a/docs/deepblink.networks.fcn.rst b/docs/deepblink.networks.fcn.rst
diff --git a/docs/deepblink.networks.inception.rst b/docs/deepblink.networks.inception.rst
diff --git a/docs/deepblink.networks.resnet.rst b/docs/deepblink.networks.resnet.rst
diff --git a/docs/deepblink.networks.rst b/docs/deepblink.networks.rst
@@ -7,9 +7,7 @@ Submodules
 .. toctree::
    :maxdepth: 1
 
-   deepblink.networks.fcn
-   deepblink.networks.inception
-   deepblink.networks.resnet
+   deepblink.networks.unet
 
 Module contents
 ---------------
diff --git a/docs/deepblink.networks.unet.rst b/docs/deepblink.networks.unet.rst
@@ -0,0 +1,7 @@
+deepblink.networks.unet module
+==============================
+
+.. automodule:: deepblink.networks.unet
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 setup(
     # Description
     name="deepblink",
-    version="0.0.8",
+    version="0.1.0",
     license="MIT",
     description="Threshold independent detection and localization of diffraction-limited spots.",
     long_description_content_type="text/plain",
@@ -48,14 +48,14 @@
     author_email="bastian@eichenbergers.ch, yinxiuzhan89@gmail.com",
     url="https://github.com/bbquercus/deepblink/",
     project_urls={
-        "Documentation": "https://deepblink.readthedocs.io/",
-        "Changelog": "https://deepblink.readthedocs.io/en/latest/changelog.html",
+        "Documentation": "https://github.com/BBQuercus/deepBlink/wiki",
+        "Changelog": "https://github.com/BBQuercus/deepBlink/releases",
         "Issue Tracker": "https://github.com/bbquercus/deepblink/issues",
     },
     keywords=["deep-learning", "biomedical", "image analysis", "spot detection"],
     classifiers=[
         # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
-        "Development Status :: 3 - Alpha",
+        "Development Status :: 4 - Beta",
         "Environment :: Console",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",

Original file line number	Diff line number	Diff line change
`@@ -45,4 +45,3 @@ def delayed_coordinates_pink(mask):`
`45`	`45`	`delayed_coordinates=delayed_coordinates_pink,`
`46`	`46`	`)`
`47`	`47`	`results_deepblink.to_csv("deepblink.csv")`
`48`		`-`
Original file line number	Diff line number	Diff line change
`@@ -44,4 +44,3 @@ def model_loader_detnet(fname):`
`44`	`44`	`delayed_coordinates=delayed_coordinates,`
`45`	`45`	`)`
`46`	`46`	`results_detnet.to_csv("detnet.csv")`
`47`		`-`
Original file line number	Diff line number	Diff line change
`@@ -126,7 +126,7 @@ def _add_utils(parser: argparse.ArgumentParser):`
`126`	`126`	`"-V",`
`127`	`127`	`"--version",`
`128`	`128`	`action="version",`
`129`		`- version="%(prog)s 0.0.8",`
	`129`	`+ version="%(prog)s 0.1.0",`
`130`	`130`	`help="Show %(prog)s's version number.",`
`131`	`131`	`)`
`132`	`132`	`group.add_argument(`