Merge pull request #230 from murthylab/cleanup

Major gui refactoring

.conda/meta.yaml

@@ -28,6 +28,7 @@ requirements:
     - scikit-learn
     - h5py
     - pandas
+    - Pillow
     - Shapely
     - psutil
     - pyzmq
@@ -46,10 +47,13 @@ requirements:
     - scikit-learn
     - h5py
     - pandas
+    - Pillow
     - Shapely
     - psutil
     - pyzmq
     - pyyaml
     - python-rapidjson
     - pip
 
+  run_constrained:
+    - pyqt ==9999999999

dev_requirements.txt

@@ -4,4 +4,6 @@ pytest-cov
 ipython
 sphinx
 sphinx_rtd_theme
-coveralls
+coveralls
+black
+pre-commit

environment.yml

@@ -10,6 +10,7 @@ dependencies:
 - scikit-learn
 - h5py
 - pandas
+- Pillow
 - Shapely
 - psutil
 - pyzmq

sleap/config/active.yaml → sleap/config/inference_forms.yaml

@@ -110,34 +110,56 @@ expert:
 
 learning:
 
-- name: min_crop_size
-  label: Minimum crop size
-  type: list
-  dtype: int
-  options: 0,64,128,256,512
-  default: 0
-
-- name: negative_samples
-  label: Negative samples
-  type: int
-  default: 20
-  range: 0,1000
+- name: _multi_instance_mode
+  label: Multi-Instance Mode
+  type: stacked
+  default: multi-instance
+  options: multi-instance,single-instance
+
+  multi-instance:
+  - name: sigma_confmaps
+    label: Sigma for confmaps
+    type: double
+    default: 5.0
+
+  - name: sigma_pafs
+    label: Sigma for pafs
+    type: double
+    default: 5.0
+
+  single-instance:
+  - name: sigma_confmaps
+    label: Sigma for confmaps
+    type: double
+    default: 5.0
+
+- name: _region_proposal_mode
+  label: Region Proposal Mode
+  type: stacked
+  default: crop
+  options: crop,full_frame
+
+  crop:
+  - name: min_crop_size
+    label: Minimum crop size
+    type: list
+    dtype: int
+    options: 0,64,128,256,512
+    default: 0
+
+  - name: negative_samples
+    label: Negative samples
+    type: int
+    default: 20
+    range: 0,1000
+
+  full_frame:
 
 - name: batch_size
   label: Batch Size
   type: int
   default: 2
 
-- name: sigma_confmaps
-  label: Sigma for confmaps
-  type: double
-  default: 5.0
-
-- name: sigma_pafs
-  label: Sigma for pafs
-  type: double
-  default: 5.0
-
 - name: _predict_frames
   label: Predict On
   type: list

sleap/config/suggestions.yaml

@@ -36,7 +36,7 @@ main:
   - name: pca_components
     label: Number of PCA components
     type: int
-    default: 50
+    default: 5
   hog:
   - name: clusters
     label: Number of clusters
@@ -53,7 +53,7 @@ main:
   - name: pca_components
     label: Number of PCA components
     type: int
-    default: 50
+    default: 5
   brisk:
   - name: clusters
     label: Number of clusters
@@ -71,7 +71,7 @@ main:
   - name: pca_components
     label: Number of PCA components
     type: int
-    default: 50
+    default: 5
   proofreading:
   - name: score_limit
     label: Low score (lt)