Miscellaneous QOL (#467)

Pre-1.1.0 update features (changelist in #467)

.conda/bld.bat

@@ -38,6 +38,7 @@ pip install jsmin
 pip install seaborn
 pip install pykalman==0.9.5
 pip install segmentation-models==1.0.1
+pip install rich==9.10.0
 
 rem # Use and update environment.yml call to install pip dependencies. This is slick.
 rem # While environment.yml contains the non pip dependencies, the only thing left

.conda/build.sh

@@ -36,6 +36,7 @@ pip install jsmin
 pip install seaborn
 pip install pykalman==0.9.5
 pip install segmentation-models==1.0.1
+pip install rich==9.10.0
 
 pip install setuptools-scm
 

docs/conf.py

@@ -89,15 +89,13 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_theme_options = {
-    'font_size': '15px'
-}
+html_theme_options = {"font_size": "15px"}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

requirements.txt

@@ -22,4 +22,5 @@ qimage2ndarray==1.8
 jsmin
 seaborn
 pykalman==0.9.5
-segmentation-models==1.0.1
+segmentation-models==1.0.1
+rich==9.10.0

setup.py

@@ -17,7 +17,7 @@
 # Get the sleap version
 with open(path.join(here, "sleap/version.py")) as f:
     version_file = f.read()
-    sleap_version = re.search("\d.+(?=['\"])", version_file).group(0)
+    sleap_version = re.search('__version__ = "([0-9\\.a]+)"', version_file).group(1)
 
 
 def get_requirements(require_name=None):
@@ -31,11 +31,13 @@ def get_requirements(require_name=None):
     version=sleap_version,
     setup_requires=["setuptools_scm"],
     install_requires=get_requirements(),
-    extras_require={"dev": get_requirements("dev"),},
-    description="SLEAP (Social LEAP Estimates Animal Pose) is a deep learning framework for estimating animal pose.",
+    extras_require={
+        "dev": get_requirements("dev"),
+    },
+    description="SLEAP (Social LEAP Estimates Animal Poses) is a deep learning framework for animal pose tracking.",
     long_description=long_description,
     long_description_content_type="text/x-rst",
-    author="Talmo Pereira, David Turner, Nat Tabris",
+    author="Talmo Pereira, Arie Matsliah, David Turner, Nat Tabris",
     author_email="[email protected]",
     project_urls={
         "Documentation": "https://sleap.ai/#sleap",

sleap/__init__.py

@@ -5,8 +5,9 @@
 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
 
 # Import submodules we want available at top-level
+from sleap.version import __version__, versions
 from sleap.io.dataset import Labels, load_file
-from sleap.io.video import Video
+from sleap.io.video import Video, load_video
 from sleap.instance import LabeledFrame, Instance, PredictedInstance, Track
 from sleap.skeleton import Skeleton
 import sleap.nn
@@ -15,4 +16,4 @@
 from sleap.nn.inference import load_model
 from sleap.nn.system import use_cpu_only, disable_preallocation
 from sleap.nn.system import summary as system_summary
-from sleap.version import __version__
+from sleap.nn.config import TrainingJobConfig, load_config

sleap/config/shortcuts.yaml

@@ -1,7 +1,7 @@
 add instance: Ctrl+I
 add videos: Ctrl+A
 clear selection: Esc
-close: QKeySequence.Close
+close: Ctrl+Q
 color predicted: 
 delete area: Ctrl+K
 delete clip:
@@ -11,19 +11,19 @@ export clip:
 fit: Ctrl+=
 goto frame: Ctrl+J
 goto marked: Ctrl+Shift+M
-goto next suggestion: QKeySequence.FindNext
+goto next suggestion: Space
 goto next track spawn: Ctrl+E
-goto next user: Ctrl+>
-goto next labeled: Ctrl+.
-goto prev suggestion: QKeySequence.FindPrevious
-goto prev labeled: 
+goto next user: Ctrl+U
+goto next labeled: Alt+Right
+goto prev suggestion: Shift+Space
+goto prev labeled: Alt+Left
 learning: Ctrl+L
 mark frame: Ctrl+M
 new: Ctrl+N
 next video: QKeySequence.Forward
 open: Ctrl+O
 prev video: QKeySequence.Back
-save as: QKeySequence.SaveAs
+save as: Ctrl+Shift+S
 save: Ctrl+S
 select next: '`'
 select to frame: Ctrl+Shift+J
@@ -33,7 +33,7 @@ show trails:
 transpose: Ctrl+T
 frame next: Right
 frame prev: Left
-frame next medium step: Down
-frame prev medium step: Up
-frame next large step: Space
-frame prev large step: /
+frame next medium step: Ctrl+Right
+frame prev medium step: Ctrl+Left
+frame next large step: Ctrl+Alt+Right
+frame prev large step: Ctrl+Alt+Left

sleap/config/training_editor_form.yaml

@@ -466,6 +466,13 @@ augmentation:
   label: Scale Max
   name: optimization.augmentation_config.scale_max
   type: double
+- label: Random flip
+  default: none
+  type: list
+  name: optimization.augmentation_config.random_flip
+  options: none,horizontal,vertical
+  default: none
+  help: 'Randomly reflect images and instances. IMPORTANT: Left/right symmetric nodes must be indicated in the skeleton or this will lead to incorrect results!'
 - default: false
   help: If True, uniformly distributed noise will be added to the image. This is effectively
     adding a different random value to each pixel to simulate shot noise. See `imgaug.augmenters.arithmetic.AddElementwise`.
@@ -533,17 +540,6 @@ augmentation:
   label: Brightness Max Val
   name: optimization.augmentation_config.brightness_max_val
   type: double
-- name: optimization.augmentation_config.random_flip
-  label: Random flip
-  help: 'Randomly reflect images and instances. IMPORTANT: Left/right symmetric nodes must be indicated in the skeleton or this will lead to incorrect results!'
-  type: bool
-  default: false
-- name: optimization.augmentation_config.flip_horizontal
-  label: Flip left/right
-  help: Flip images horizontally when randomly reflecting. If unchecked, flipping will
-    reflect images up/down.
-  type: bool
-  default: true
 
 optimization:
 - default: 8