diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index b69ea56d9940c0e6600787165c02f7f98c03afc7..91add3dafa0d6ed069f046e74ca3973c34540e04 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -557,18 +557,12 @@ class Tiler(ProcessABC):
item: string
The channel
"""
-
- # pattern = re.compile(f"*{item}*", re.IGNORECASE)
- for i, ch in enumerate(self.channels):
- found = re.match(item, ch, re.IGNORECASE)
- if found:
- if len(found.string) - (found.endpos - found.start()):
- print(f"WARNING: channel {item} matched {ch} using regex")
- return i
-
- raise Warning(
- f"Reference channel {item} not in the available channels: {self.channels}"
- )
+ channel = find_channel_index(self.channels, item)
+ if channel is None:
+ raise Warning(
+ f"Reference channel {channel} not in the available channels: {self.channels}"
+ )
+ return channel
@staticmethod
def ifoob_pad(full, slices):
@@ -610,3 +604,24 @@ class Tiler(ProcessABC):
# pad tile with median value of trap image
trap = np.pad(trap, [[0, 0]] + padding.tolist(), "median")
return trap
+
+
+def find_channel_index(image_channels: t.List[str], channel: str):
+ """
+ Access
+ """
+ for i, ch in enumerate(image_channels):
+ found = re.match(channel, ch, re.IGNORECASE)
+ if found:
+ if len(found.string) - (found.endpos - found.start()):
+ print(f"WARNING: channel {channel} matched {ch} using regex")
+ return i
+
+
+def find_channel_name(image_channels: t.List[str], channel: str):
+ """
+ Find the name of the channel according to a given channel regex.
+ """
+ index = find_channel_index(image_channels, channel)
+ if index is not None:
+ return image_channels[index]
diff --git a/src/extraction/core/extractor.py b/src/extraction/core/extractor.py
index e94bdc4be87c4bbcb8748bac29b84305f4f27ba1..6a5af6bcbfef415ede6d3c0b2ca70b276c86bcb0 100644
--- a/src/extraction/core/extractor.py
+++ b/src/extraction/core/extractor.py
@@ -579,7 +579,7 @@ class Extractor(ProcessABC):
"""
if channels is None:
channels = (*self.params.tree,)
- if channel in channels:
+ if channel in channels: # TODO start here to fetch channel using regex
return traps[:, channels.index(channel), 0]
elif channel in self.img_bgsub:
return self.img_bgsub[channel]
diff --git a/src/extraction/core/functions/defaults.py b/src/extraction/core/functions/defaults.py
index c5b520f1180f720da2304f9ba91aa5f94ebb656c..e67ffa19d09d0b7370afd1e4b63d8e28631366fe 100644
--- a/src/extraction/core/functions/defaults.py
+++ b/src/extraction/core/functions/defaults.py
@@ -1,4 +1,5 @@
# File with defaults for ease of use
+import re
import typing as t
from pathlib import PosixPath
@@ -9,7 +10,8 @@ def exparams_from_meta(
meta: t.Union[dict, PosixPath, str], extras: t.Collection[str] = ["ph"]
):
"""
- Obtain parameters from metadata of hdf5 file
+ Obtain parameters from metadata of hdf5 file.
+ It compares a list of candidate channels using case-inspecific REGEX to identify valid channels.
"""
meta = meta if isinstance(meta, dict) else load_attributes(meta)
base = {
@@ -23,6 +25,7 @@ def exparams_from_meta(
"GFPFast",
"mCherry",
"pHluorin405",
+ "pHluorin488",
"Flavin",
"Cy5",
"mKO2",
@@ -35,32 +38,61 @@ def exparams_from_meta(
"std",
"imBackground",
"max5px",
- "nuc_est_conv",
+ # "nuc_est_conv",
}
- default_rm = {r: default_metrics for r in default_reductions}
+ # Defined ratiometric combinations that can be used as ratio
+ # key is numerator and value is denominator; add more to support additional channel names
+ ratiometric_combinations = {"phluorin405": ("phluorin488", "gfpfast")}
+
+ default_reduction_metrics = {
+ r: default_metrics for r in default_reductions
+ }
# default_rm["None"] = ["nuc_conv_3d"] # Uncomment this to add nuc_conv_3d (slow)
- av_flch = candidate_channels.intersection(
- meta["channels/channel"]
- ).difference({"Brightfield", "DIC", "BrightfieldGFP"})
+ from aliby.tile.tiler import find_channel_name
+
+ extant_fluorescence_ch = []
+ for av_channel in candidate_channels:
+ # Find channels in metadata whose names match
+ found_channel = find_channel_name(meta["channels/channel"], av_channel)
+ if found_channel is not None:
+ extant_fluorescence_ch.append(found_channel)
- for ch in av_flch:
- base["tree"][ch] = default_rm
+ for ch in extant_fluorescence_ch:
+ base["tree"][ch] = default_reduction_metrics
- base["sub_bg"] = av_flch
+ base["sub_bg"] = extant_fluorescence_ch
# Additional extraction defaults when channels available
if "ph" in extras:
- if {"pHluorin405", "GFPFast"}.issubset(av_flch):
+ # SWAINLAB-specific names
+ # find first valid combination of ratiometric fluorescence channels
+ numerator_channel, denominator_channel = (None, None)
+ for ch1, chs2 in ratiometric_combinations.items():
+ found_channel1 = find_channel_name(extant_fluorescence_ch, ch1)
+ if found_channel1 is not None:
+ numerator_channel = found_channel1
+ for ch2 in chs2:
+ found_channel2 = find_channel_name(
+ extant_fluorescence_ch, ch2
+ )
+ if found_channel2:
+ denominator_channel = found_channel2
+ break
+ # If two compatible pHluorin channels are available
+ if numerator_channel is not None and denominator_channel is not None:
sets = {
b + a: (x, y)
for a, x in zip(
["", "_bgsub"],
(
- ["GFPFast", "pHluorin405"],
- ["GFPFast_bgsub", "pHluorin405_bgsub"],
+ [numerator_channel, denominator_channel],
+ [
+ f"{numerator_channel}_bgsub",
+ f"{denominator_channel}_bgsub",
+ ],
),
)
for b, y in zip(["em_ratio", "gsum"], ["div0", "add"])
@@ -68,7 +100,7 @@ def exparams_from_meta(
for i, v in sets.items():
base["multichannel_ops"][i] = [
*v,
- default_rm,
+ default_reduction_metrics,
]
return base