add test for stack.utils

fish-quant · May 5, 2020 · c5ce909 · c5ce909
1 parent ab94c2b
commit c5ce909
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Showing 9 changed files with 449 additions and 66 deletions.
diff --git a/tests/tests.py → .codecov.yml b/tests/tests.py → .codecov.yml
diff --git a/bigfish/stack/__init__.py b/bigfish/stack/__init__.py
@@ -1,13 +1,13 @@
 # -*- coding: utf-8 -*-
 
 """
-The bigfish.stack module includes function to read data, preprocess them and
+The bigfish.stack module includes functions to read data, preprocess them and
 build stack of images.
 """
 
 from .utils import (check_array, check_df, check_recipe, check_parameter,
                     check_range_value,
-                    get_offset_value, get_eps_float32)
+                    get_margin_value, get_eps_float32)
 from .io import (read_image, read_pickle, read_cell_json, read_rna_json,
                  read_dv,
                  save_image)
@@ -42,7 +42,7 @@
 
 
 _utils = ["check_array", "check_df", "check_recipe", "check_parameter",
-          "check_range_value", "get_offset_value", "get_eps_float32"]
+          "check_range_value", "get_margin_value", "get_eps_float32"]
 
 _io = ["read_image", "read_pickle", "read_cell_json", "read_rna_json",
        "read_dv",

diff --git a/bigfish/stack/postprocess.py b/bigfish/stack/postprocess.py
@@ -8,7 +8,7 @@
 import numpy as np
 from scipy import ndimage as ndi
 
-from .utils import check_array, check_parameter, get_offset_value
+from .utils import check_array, check_parameter, get_margin_value
 
 from skimage.measure import regionprops, find_contours
 from skimage.draw import polygon_perimeter
@@ -473,7 +473,7 @@ def center_mask_coord(main, others=None):
                         dtype=[np.uint8, np.uint16, np.int64, bool])
 
     # initialize parameter
-    marge = get_offset_value()
+    marge = get_margin_value()
 
     # compute by how much we need to move the main object to center it
     if main.shape[1] == 2:
@@ -691,7 +691,7 @@ def from_coord_to_frame(coord, external_coord=True):
     check_parameter(external_coord=bool)
 
     # initialize marge
-    marge = get_offset_value()
+    marge = get_margin_value()
 
     # from 2D coordinates boundaries to binary boundaries
     if external_coord:

diff --git a/bigfish/stack/preparation.py b/bigfish/stack/preparation.py
@@ -11,7 +11,7 @@
 import pandas as pd
 from scipy import ndimage as ndi
 
-from .utils import get_offset_value
+from .utils import get_margin_value
 from .augmentation import augment
 from .preprocess import cast_img_float32
 from .filter import mean_filter
@@ -272,8 +272,8 @@ def build_image(data, id_cell, image_shape=None, coord_refinement=True,
 
     # build matrices
     if image_shape is None:
-        max_x = cyt_coord[:, 0].max() + get_offset_value()
-        max_y = cyt_coord[:, 1].max() + get_offset_value()
+        max_x = cyt_coord[:, 0].max() + get_margin_value()
+        max_y = cyt_coord[:, 1].max() + get_margin_value()
         image_shape = (max_x, max_y)
     rna = np.zeros(image_shape, dtype=np.float32)
     rna[rna_coord[:, 0], rna_coord[:, 1]] = 1.0
@@ -350,8 +350,8 @@ def _build_rna(data, id_cell, output_shape=None):
     # get current shape
     cyt_coord = data.loc[id_cell, "pos_cell"]
     cyt_coord = np.array(cyt_coord, dtype=np.int64)
-    max_x = cyt_coord[:, 0].max() + get_offset_value()
-    max_y = cyt_coord[:, 1].max() + get_offset_value()
+    max_x = cyt_coord[:, 0].max() + get_margin_value()
+    max_y = cyt_coord[:, 1].max() + get_margin_value()
     input_shape = (max_x, max_y)
 
     if output_shape is not None: