From 14fb24f496c71131ff72756dd4caa2c8c36b7d8a Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Fri, 21 Jun 2019 16:54:03 +0200
Subject: [PATCH] Change to ne file-paths in tests
---
test/attributes/test_base.py | 4 ++--
test/attributes/test_genes.py | 6 +++---
test/attributes/test_morphology.py | 16 ++++++++--------
3 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/test/attributes/test_base.py b/test/attributes/test_base.py
index 00dba67..7d3b4e1 100644
--- a/test/attributes/test_base.py
+++ b/test/attributes/test_base.py
@@ -17,10 +17,10 @@ class TestGeneAttributes(unittest.TestCase):
except OSError:
pass
- def test_genes(self):
+ def test_base_attributes(self):
from scripts.attributes.base_attributes import base_attributes
- input_path = '../../data/0.0.0/segmentations/em-segmented-nuclei-labels.h5'
+ input_path = '../../data/0.0.0/segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.h5'
input_key = 't00000/s00/0/cells'
output_path = os.path.join(self.tmp_folder, 'table-test.csv')
target = 'local'
diff --git a/test/attributes/test_genes.py b/test/attributes/test_genes.py
index a0a1ca6..8ceb547 100644
--- a/test/attributes/test_genes.py
+++ b/test/attributes/test_genes.py
@@ -29,14 +29,14 @@ class TestGeneAttributes(unittest.TestCase):
from scripts.files import get_h5_path_from_xml
# load original genes table
- original_table_file = '../../data/0.0.0/tables/em-segmented-cells-labels/genes.csv'
+ original_table_file = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv'
original_table = self.load_table(original_table_file)
self.assertEqual(original_table.dtype, np.dtype('float32'))
labels = original_table[:, 0].astype('uint64')
# compute and load the genes table
- segm_file = '../../data/0.0.0/segmentations/em-segmented-cells-labels.h5'
- genes_file = '../../data/0.0.0/misc/meds_all_genes.xml'
+ segm_file = '../../data/0.0.0/segmentations/sbem-6dpf-1-whole-segmented-cells-labels.h5'
+ genes_file = '../../data/0.0.0/misc/prospr-6dpf-1-whole_meds_all_genes.xml'
genes_file = get_h5_path_from_xml(genes_file)
table_file = self.test_file
diff --git a/test/attributes/test_morphology.py b/test/attributes/test_morphology.py
index 93207c7..f074e6d 100644
--- a/test/attributes/test_morphology.py
+++ b/test/attributes/test_morphology.py
@@ -37,12 +37,12 @@ class TestMorphologyAttributes(unittest.TestCase):
self.write_global_config(MorphologyWorkflow.get_config()['global'])
- raw_path = '../../data/0.0.0/images/em-raw-full-res.xml'
+ raw_path = '../../data/0.0.0/images/sbem-6dpf-1-whole-raw.xml'
raw_path = get_h5_path_from_xml(raw_path)
# compute and load the morpho table
- seg_path = '../../data/0.0.0/segmentations/em-segmented-nuclei-labels.h5'
- table_in_path = '../../data/0.0.0/tables/em-segmented-nuclei-labels/default.csv'
+ seg_path = '../../data/0.0.0/segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.h5'
+ table_in_path = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv'
table_out_path = os.path.join(self.tmp_folder, 'table_nuclei.csv')
res = [.1, .08, .08]
n_labels = np.genfromtxt(table_in_path, delimiter='\t', skip_header=1).shape[0]
@@ -53,7 +53,7 @@ class TestMorphologyAttributes(unittest.TestCase):
table = self.load_table(table_out_path)
# load original table, make sure new and old table agree
- original_table_file = '../../data/0.0.0/tables/em-segmented-nuclei-labels/morphology.csv'
+ original_table_file = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv'
original_table = self.load_table(original_table_file)
self.assertEqual(table.shape, original_table.shape)
self.assertTrue(np.allclose(table, original_table))
@@ -65,9 +65,9 @@ class TestMorphologyAttributes(unittest.TestCase):
self.write_global_config(MorphologyWorkflow.get_config()['global'])
# compute and load the morpho table
- seg_path = '../../data/0.0.0/segmentations/em-segmented-cells-labels.h5'
- mapping_path = '../../data/0.0.0/tables/em-segmented-cells-labels/objects.csv'
- table_in_path = '../../data/0.0.0/tables/em-segmented-cells-labels/default.csv'
+ seg_path = '../../data/0.0.0/segmentations/sbem-6dpf-1-whole-segmented-cells-labels.h5'
+ mapping_path = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/objects.csv'
+ table_in_path = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv'
table_out_path = os.path.join(self.tmp_folder, 'table_cells.csv')
res = [.025, .02, .02]
n_labels = np.genfromtxt(table_in_path, delimiter='\t', skip_header=1).shape[0]
@@ -78,7 +78,7 @@ class TestMorphologyAttributes(unittest.TestCase):
table = self.load_table(table_out_path)
# make sure new and old table agree
- original_table_file = '../../data/0.0.0/tables/em-segmented-cells-labels/morphology.csv'
+ original_table_file = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/morphology.csv'
original_table = self.load_table(original_table_file)
self.assertEqual(table.shape, original_table.shape)
self.assertTrue(np.allclose(table, original_table))
--
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