Merge pull request #60 from fish-quant/multistack

Multistack subpackage

bigfish/detection/__init__.py

@@ -7,6 +7,8 @@
 and 3-d.
 """
 
+# TODO adapt to float64 coordinates
+
 from .spot_detection import detect_spots
 from .spot_detection import local_maximum_detection
 from .spot_detection import spots_thresholding
@@ -29,6 +31,7 @@
 
 from .snr import compute_snr_spots
 
+from .utils import convert_spot_coordinates
 
 _spots = [
     "detect_spots",
@@ -57,4 +60,7 @@
 _snr = [
     "compute_snr_spots"]
 
-__all__ = _spots + _dense + _model + _clusters + _snr
+_utils = [
+    "convert_spot_coordinates"]
+
+__all__ = (_spots + _dense + _model + _clusters + _snr + _utils)

bigfish/detection/cluster_detection.py

@@ -10,6 +10,7 @@
 import numpy as np
 import bigfish.stack as stack
 from sklearn.cluster import DBSCAN
+from .utils import convert_spot_coordinates
 
 
 # ### Detect clusters ###
@@ -87,38 +88,6 @@ def detect_clusters(spots, voxel_size_z=None, voxel_size_yx=100, radius=350,
     return clustered_spots, clusters
 
 
-def _convert_spot_coordinates(spots, voxel_size_z, voxel_size_yx):
-    """Convert spots coordinates from pixel to nanometer.
-
-    Parameters
-    ----------
-    spots : np.ndarray, np.int64
-        Coordinates of the detected spots with shape (nb_spots, 3) or
-        (nb_spots, 2).
-    voxel_size_z : int or float
-        Height of a voxel, along the z axis, in nanometer.
-    voxel_size_yx : int or float
-        Size of a voxel on the yx plan, in nanometer.
-
-    Returns
-    -------
-    spots_nanometer : np.ndarray, np.int64
-        Coordinates of the detected spots with shape (nb_spots, 3) or
-        (nb_spots, 3), in nanometer.
-
-    """
-    # convert spots coordinates in nanometer
-    spots_nanometer = spots.copy()
-    if spots.shape[1] == 3:
-        spots_nanometer[:, 0] *= voxel_size_z
-        spots_nanometer[:, 1:] *= voxel_size_yx
-
-    else:
-        spots_nanometer *= voxel_size_yx
-
-    return spots_nanometer
-
-
 def _cluster_spots(spots, voxel_size_z, voxel_size_yx, radius, nb_min_spots):
     """Assign a cluster to each spot.
 
@@ -149,9 +118,9 @@ def _cluster_spots(spots, voxel_size_z, voxel_size_yx, radius, nb_min_spots):
 
     """
     # convert spots coordinates in nanometer
-    spots_nanometer = _convert_spot_coordinates(spots=spots,
-                                                voxel_size_z=voxel_size_z,
-                                                voxel_size_yx=voxel_size_yx)
+    spots_nanometer = convert_spot_coordinates(spots=spots,
+                                               voxel_size_z=voxel_size_z,
+                                               voxel_size_yx=voxel_size_yx)
 
     # fit a DBSCAN clustering algorithm with a specific radius
     dbscan = DBSCAN(eps=radius, min_samples=nb_min_spots)

bigfish/detection/utils.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
+
+"""
+Utility functions for bigfish.detection subpackage.
+"""
+
+
+def convert_spot_coordinates(spots, voxel_size_z, voxel_size_yx):
+    """Convert spots coordinates from pixel to nanometer.
+
+    Parameters
+    ----------
+    spots : np.ndarray, np.int64
+        Coordinates of the detected spots with shape (nb_spots, 3) or
+        (nb_spots, 2).
+    voxel_size_z : int or float
+        Height of a voxel, along the z axis, in nanometer.
+    voxel_size_yx : int or float
+        Size of a voxel on the yx plan, in nanometer.
+
+    Returns
+    -------
+    spots_nanometer : np.ndarray, np.int64
+        Coordinates of the detected spots with shape (nb_spots, 3) or
+        (nb_spots, 3), in nanometer.
+
+    """
+    # convert spots coordinates in nanometer
+    spots_nanometer = spots.copy()
+    if spots.shape[1] == 3:
+        spots_nanometer[:, 0] *= voxel_size_z
+        spots_nanometer[:, 1:] *= voxel_size_yx
+
+    else:
+        spots_nanometer *= voxel_size_yx
+
+    return spots_nanometer

bigfish/multistack/__init__.py

@@ -0,0 +1,48 @@
+# -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
+
+"""
+The bigfish.multistack subpackage includes function to process input and output
+from different channels.
+"""
+
+from .utils import check_recipe
+from .utils import check_datamap
+
+from .preprocess import build_stacks
+from .preprocess import build_stack
+from .preprocess import build_stack_no_recipe
+
+from .colocalization import detect_spots_colocalization
+from .colocalization import get_elbow_value_colocalized
+
+from .cell_extraction import identify_objects_in_region
+from .cell_extraction import remove_transcription_site
+from .cell_extraction import match_nuc_cell
+from .cell_extraction import extract_cell
+from .cell_extraction import extract_spots_from_frame
+from .cell_extraction import summarize_extraction_results
+
+_utils = [
+    "check_recipe",
+    "check_datamap"]
+
+_preprocess = [
+    "build_stacks",
+    "build_stack",
+    "build_stack_no_recipe"]
+
+_colocalization = [
+    "detect_spots_colocalization",
+    "get_elbow_value_colocalized"]
+
+_postprocess = [
+    "identify_objects_in_region",
+    "remove_transcription_site",
+    "match_nuc_cell",
+    "extract_cell",
+    "extract_spots_from_frame",
+    "summarize_extraction_results"]
+
+__all__ = _utils + _preprocess + _colocalization + _postprocess