diff --git a/environment.yaml b/environment.yaml index aeb5ea7be91282b1757473af95b261d0cdf80813..a6a862298b33629f37bb4a455d284b078342a0fc 100644 --- a/environment.yaml +++ b/environment.yaml @@ -16,3 +16,4 @@ dependencies: - scikit-learn - vigra - z5py + - mahotas diff --git a/mmpb/extension/attributes/morphology.py b/mmpb/extension/attributes/morphology.py index 24d98934bc06fd68767bbb87b80fbb118b6b59d6..e8d9be95c4feede626343e1897851e63503c375f 100644 --- a/mmpb/extension/attributes/morphology.py +++ b/mmpb/extension/attributes/morphology.py @@ -36,11 +36,11 @@ class MorphologyBase(luigi.Task): # if the raw path is None, we don't compute intensity features raw_path = luigi.Parameter(default=None) # we always need the nucleus segmentation - nucleus_segmentation_path = luigi.Paramter() + nucleus_segmentation_path = luigi.Parameter() # we only need the cell segmentation if we compute cell morphology features cell_segmentation_path = luigi.Parameter(default=None) # we only need the chromatin segmentation if we compute nucleus features - chromatin_segmentation_path = luigi.Paramter(default=None) + chromatin_segmentation_path = luigi.Parameter(default=None) # the scale used for computation, relative to the raw scale scale = luigi.IntParameter(default=3) @@ -49,8 +49,8 @@ class MorphologyBase(luigi.Task): # nucleus mapping table and the region mapping table in_table_path = luigi.Parameter() # only need the mapping paths for the nucleus features - nucleus_mapping_path = luigi.Paramter(default=None) - region_mapping_path = luigi.Paramter(default=None) + nucleus_mapping_path = luigi.Parameter(default=None) + region_mapping_path = luigi.Parameter(default=None) # prefix for the output tables output_prefix = luigi.Parameter() diff --git a/mmpb/extension/attributes/workflow.py b/mmpb/extension/attributes/workflow.py index 741c906acc74946aea2739e2e4e595f483130ce0..c3ca4d334ba870accef4dc69a43c396d52e67924 100644 --- a/mmpb/extension/attributes/workflow.py +++ b/mmpb/extension/attributes/workflow.py @@ -43,11 +43,11 @@ class MorphologyWorkflow(WorkflowBase): # if the raw path is None, we don't compute intensity features raw_path = luigi.Parameter(default=None) # we always need the nucleus segmentation - nucleus_segmentation_path = luigi.Paramter() + nucleus_segmentation_path = luigi.Parameter() # we only need the cell segmentation if we compute cell morphology features cell_segmentation_path = luigi.Parameter(default=None) # we only need the chromatin segmentation if we compute nucleus features - chromatin_segmentation_path = luigi.Paramter(default=None) + chromatin_segmentation_path = luigi.Parameter(default=None) # the scale used for computation, relative to the raw scale scale = luigi.IntParameter(default=3) @@ -56,15 +56,15 @@ class MorphologyWorkflow(WorkflowBase): # nucleus mapping table and the region mapping table in_table_path = luigi.Parameter() # only need the mapping paths for the nucleus features - nucleus_mapping_path = luigi.Paramter(default=None) - region_mapping_path = luigi.Paramter(default=None) + nucleus_mapping_path = luigi.Parameter(default=None) + region_mapping_path = luigi.Parameter(default=None) # minimum and maximum sizes for objects / bounding box min_size = luigi.IntParameter() max_size = luigi.IntParameter(default=None) max_bb = luigi.IntParameter() - output_path = luigi.Paramter() + output_path = luigi.Parameter() def requires(self): out_prefix = os.path.join(self.tmp_folder, 'sub_table_%s' % self.prefix)