From 0a09e6828d67a95689aadeb5234fe55926bbe9d2 Mon Sep 17 00:00:00 2001
From: alan <alan@Arran.bio.ed.ac.uk>
Date: Tue, 6 Sep 2022 17:59:09 +0100
Subject: [PATCH] refactor(tiler,ext): get_traps->get_tiles
---
README.md | 2 +-
aliby/tile/tiler.py | 10 +++++++++-
aliby/utils/imageViewer.py | 2 +-
extraction/core/extractor.py | 7 ++++---
4 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 6d330a9d..fac23288 100644
--- a/README.md
+++ b/README.md
@@ -105,7 +105,7 @@ Alternatively, if you want to get all the traps at a given timepoint:
```python
timepoint = 0
-seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None,
+seg_expt.get_tiles_timepoints(timepoint, tile_size=96, channels=None,
z=[0,1,2,3,4])
```
diff --git a/aliby/tile/tiler.py b/aliby/tile/tiler.py
index 80402541..2740022a 100644
--- a/aliby/tile/tiler.py
+++ b/aliby/tile/tiler.py
@@ -488,8 +488,16 @@ class Tiler(ProcessABC):
self.run_tp(frame)
return None
+ def get_traps_timepoint(self, *args, **kwargs):
+ #
+ print(
+ DeprecationWarning("Deprecated:Use get_tiles_timepoint instead.")
+ )
+
+ return self.get_tiles_timepoint(*args, **kwargs)
+
# The next set of functions are necessary for the extraction object
- def get_traps_timepoint(
+ def get_tiles_timepoint(
self, tp, tile_shape=None, channels=None, z=None
) -> np.ndarray:
"""
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index d53b4f0e..67490812 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -197,7 +197,7 @@ class remoteImageViewer:
# tps = set(tps).difference(self.full.keys())
for ch, tp in ch_tps:
if (ch, tp) not in self.full:
- self.full[(ch, tp)] = self.tiler.get_traps_timepoint(
+ self.full[(ch, tp)] = self.tiler.get_tiles_timepoint(
tp, channels=[ch], z=[z]
)[:, 0, 0, ..., z]
requested_trap = {tp: self.full[(ch, tp)] for ch, tp in ch_tps}
diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py
index ee7e58b6..b5886782 100644
--- a/extraction/core/extractor.py
+++ b/extraction/core/extractor.py
@@ -256,7 +256,7 @@ class Extractor(ProcessABC):
z = list(range(self.tiler.shape[-1]))
# gets the data via tiler
traps = (
- self.tiler.get_traps_timepoint(
+ self.tiler.get_tiles_timepoint(
tp, channels=channel_ids, z=z, **kwargs
)
if channel_ids
@@ -294,7 +294,8 @@ class Extractor(ProcessABC):
A two-tuple of a tuple of results and a tuple with the corresponding trap_id and cell labels
"""
if labels is None:
- raise Warning("No labels given. Sorting cells using index.")
+ print("Warning: No labels given. Sorting cells using index.")
+
cell_fun = True if metric in self._all_cell_funs else False
idx = []
results = []
@@ -471,7 +472,7 @@ class Extractor(ProcessABC):
# find image data at the time point
# stored as an array arranged as (traps, channels, timepoints, X, Y, Z)
# Alan: traps does not appear the best name here!
- traps = self.get_traps(tp, tile_shape=tile_size, channels=tree_chs)
+ traps = self.get_tiles(tp, tile_shape=tile_size, channels=tree_chs)
# generate boolean masks for background as a list with one mask per trap
if self.params.sub_bg:
--
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