finish stubbing out tests for the data loader

vanvalenlab · May 13, 2020 · 9cad1b0 · 9cad1b0
1 parent f8b4688
commit 9cad1b0
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Showing 2 changed files with 43 additions and 42 deletions.
diff --git a/caliban_toolbox/pre_annotation/data_loader.py b/caliban_toolbox/pre_annotation/data_loader.py
@@ -78,7 +78,7 @@ def __init__(self,
                  imaging_types,
                  specimen_types,
                  compartments=None,
-                 markers=['all'],  # these and the following should be sets to prevent double 'all's etc
+                 markers=['all'],  # the following should be sets to prevent double 'alls etc
                  exp_ids=['all'],
                  sessions=['all'],
                  positions=['all'],
@@ -184,11 +184,11 @@ def _path_builder(self, root_path, list_of_dirs):
            and verify that these new paths exist.
 
         Args:
-            root_path (path):
-            list_of_dirs (list):
+            root_path (path): base path to add to
+            list_of_dirs (list): directory names to add to the base path
 
         Returns:
-            list:
+            list: combined path of length equal to number of dirs in list_of_dirs
         """
         new_paths = []
         for item in list_of_dirs:
@@ -202,7 +202,8 @@ def _path_builder(self, root_path, list_of_dirs):
         return new_paths
 
     def _assemble_paths(self):
-        """
+        """Go through permuations of parameters and assemble paths that lead to the
+           directories of interest (containing a metadata json file) as well as img stacks
         """
         # maybe a dictionary would be better here? need to map multiple tiff files to a data dir
         # probably should be a class per dataset
@@ -458,4 +459,4 @@ def load_imagedata(self):
 
         # predict on data
         # need to have a dictionary of models to run
-        # curate-seg-track job
+        # curate-seg-track job
diff --git a/caliban_toolbox/pre_annotation/data_loader_test.py b/caliban_toolbox/pre_annotation/data_loader_test.py
@@ -29,52 +29,52 @@
 from __future__ import division
 from __future__ import print_function
 
-import os
-
-import numpy as np
-import pandas as pd
-import skimage as sk
+import random
 
 import pytest
 
 from caliban_toolbox.pre_annotation import data_loader
 
+
 def _get_dummy_inputs(object):
-    possible_data_type = [['2d', 'static'], ['2d', 'dynamic'], ['3d', 'static'], ['3d', 'dynamic']]
-    possible_imaging_types = [[]]
-    possible_specimen_types
-    possible_compartments=None
-    possible_markers=['all']
-    possible_exp_ids=['all']
-    possible_sessions=['all']
-    possible_positions=['all']
-    possible_file_type='.tif'
+    possible_data_type = random.choice([['2d', 'static'],
+                                        ['2d', 'dynamic'],
+                                        ['3d', 'static'],
+                                        ['3d', 'dynamic']])
+    possible_imaging_types = random.choice([['fluo'], ['phase'], ['fluo', 'phase'], ['all']])
+    possible_specimen_types = random.choice([['HEK293'], ['HeLa'], ['HEK293', 'HeLa'], ['all']])
+    possible_compartments = random.choice([[None], ['nuclear'], ['nuclear', 'wholecell'], ['all']])
+    possible_markers = ['all']
+    possible_exp_ids = ['all']
+    possible_sessions = ['all']
+    possible_positions = ['all']
+    possible_file_type = '.tif'
+
+    loader_inputs = [possible_data_type,
+                     possible_imaging_types,
+                     possible_specimen_types,
+                     possible_compartments,
+                     possible_markers,
+                     possible_exp_ids,
+                     possible_sessions,
+                     possible_positions,
+                     possible_file_type]
+
+    return loader_inputs
 
 
 class TestUniversalDataLoader(object):  # pylint: disable=useless-object-inheritance
 
     def test_simple(self):
         loader_inputs = _get_dummy_inputs(self)
-        _ = data_loader.UniversalDataLoader(loader_inputs)
-
-        # test data with bad rank
-        with pytest.raises(ValueError):
-            data_loader.UniversalDataLoader(
-                np.random.random((32, 32, 1)),
-                np.random.randint(num_objects, size=(32, 32, 1)),
-                model=model)
-
-        # test mismatched x and y shape
-        with pytest.raises(ValueError):
-            data_loader.UniversalDataLoader(
-                np.random.random((3, 32, 32, 1)),
-                np.random.randint(num_objects, size=(2, 32, 32, 1)),
-                model=model)
-
-        # test bad features
-        with pytest.raises(ValueError):
-            data_loader.UniversalDataLoader(x, y, model=model, features=None)
 
-        # test bad data_format
-        with pytest.raises(ValueError):
-            data_loader.UniversalDataLoader(x, y, model=model, data_format='invalid')
+        # test with standard inputs
+        _ = data_loader.UniversalDataLoader(data_type=loader_inputs[0],
+                                            imaging_types=loader_inputs[1],
+                                            specimen_types=loader_inputs[2],
+                                            compartments=loader_inputs[3],
+                                            markers=loader_inputs[4],
+                                            exp_ids=loader_inputs[5],
+                                            sessions=loader_inputs[6],
+                                            positions=loader_inputs[7],
+                                            file_type=loader_inputs[8])