diff --git a/core/processes/merger.py b/core/processes/merger.py
index 6132e72544660314ff5b188a3731aa0ec7c887bb..51a2e0a49aefade6c344eb0929d9fa7abedf6a18 100644
--- a/core/processes/merger.py
+++ b/core/processes/merger.py
@@ -1,5 +1,5 @@
from postprocessor.core.processes.base import ParametersABC, ProcessABC
-from postprocessor.core.functions.tracks import clean_tracks, merge_tracks, join_tracks
+from postprocessor.core.functions.tracks import get_joinable
class mergerParameters(ParametersABC):
@@ -52,7 +52,9 @@ class merger(ProcessABC):
super().__init__(parameters)
def run(self, signal):
- merged, _ = merge_tracks(signal) # , min_len=self.window + 1)
- indices = (*zip(*merged.index.tolist()),)
- names = merged.index.names
- return {name: ids for name, ids in zip(names, indices)}
+ joinable = get_joinable(signal)
+ # merged, _ = merge_tracks(signal) # , min_len=self.window + 1)
+ # indices = (*zip(*merged.index.tolist()),)
+ # names = merged.index.names
+ # return {name: ids for name, ids in zip(names, indices)}
+ return joinable
diff --git a/core/processes/picker.py b/core/processes/picker.py
index 8be722eb609c598f6d21f425fb8a6c798dcb53f2..ca441e4d4c6e0056af247c1ff9200262131f55af 100644
--- a/core/processes/picker.py
+++ b/core/processes/picker.py
@@ -93,6 +93,8 @@ class picker(ProcessABC):
def run(self, signals):
for alg in self.sequence:
+ if alg == "condition":
+ pass
self.signals = getattr(self, "pick_by_" + alg)(signals)
return self.signals
diff --git a/core/processor.py b/core/processor.py
index c170b53d4fbfeeaf7e2e79a774cdf8669ffcae16..c590ccd85c0a3d8093a7e7c93006d4f2ab3cd9dc 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -27,13 +27,13 @@ class PostProcessorParameters(ParametersABC):
def __init__(
self,
- processes={},
- process_parameters={},
- process_outpaths={},
+ targets={},
+ parameters={},
+ outpaths={},
):
- self.processes: Dict = processes
- self.process_parameters: Dict = process_parameters
- self.process_outpaths: Dict = process_outpaths
+ self.targets: Dict = targets
+ self.parameters: Dict = parameters
+ self.outpaths: Dict = outpaths
def __getitem__(self, item):
return getattr(self, item)
@@ -42,7 +42,7 @@ class PostProcessorParameters(ParametersABC):
def default(cls, kind=None):
if kind == "defaults" or kind == None:
return cls(
- processes={
+ targets={
"prepost": {
"merger": "/extraction/general/None/area",
"picker": ["/extraction/general/None/area"],
@@ -51,9 +51,14 @@ class PostProcessorParameters(ParametersABC):
"dsignal": ["/extraction/general/None/area"],
# "savgol": ["/extraction/general/None/area"],
},
- "process_parameters": {},
- "process_outpaths": {},
},
+ parameters={
+ "prepost": {
+ "merger": mergerParameters.default(),
+ "picker": pickerParameters.default(),
+ }
+ },
+ outpaths={},
)
def to_dict(self):
@@ -68,20 +73,20 @@ class PostProcessor:
self._writer = Writer(filename)
# self.outpaths = parameters["outpaths"]
- self.merger = merger(parameters["processes"]["prepost"]["merger"])
+ self.merger = merger(parameters["parameters"]["prepost"]["merger"])
self.picker = picker(
- parameters=parameters["processes"]["prepost"]["picker"],
+ parameters=parameters["parameters"]["prepost"]["picker"],
cells=Cells.from_source(filename),
)
- self.process_classfun = {
+ self.classfun = {
process: self.get_process(process)
- for process in parameters["processes"]["processes"].keys()
+ for process in parameters["targets"]["processes"].keys()
}
- self.process_parameters = {
+ self.parameters = {
process: self.get_parameters(process)
- for process in parameters["processes"]["processes"]
+ for process in parameters["targets"]["processes"]
}
- self.processes = parameters["processes"]
+ self.targets = parameters["targets"]
@staticmethod
def get_process(process):
@@ -103,12 +108,12 @@ class PostProcessor:
def run_prepost(self):
"""Important processes run before normal post-processing ones"""
- merge_events = self.merger.run(self._signal[self.prepost["merger"]])
+ merge_events = self.merger.run(self._signal[self.targets["prepost"]["merger"]])
- with h5py.File(self.filename, "r") as f:
+ with h5py.File(self._filename, "r") as f:
prev_idchanges = self._signal.get_id_changes()
- changes_history = prev_idchanges + merge_events + picks
+ changes_history = prev_idchanges + [merge_events] # + [picks]
self._writer.write("/id_changes", data=changes_history)
self._writer.write(
"/postprocessing/merge_events/",
@@ -116,7 +121,7 @@ class PostProcessor:
meta={"source": "/cell_info/"},
)
changes_history += picks
- picks = self.picker.run(self._signal[self.processes["picker"][0]])
+ picks = self.picker.run(self._signal[self.targets["prepost"]["picker"][0]])
# self._writer.write()
def run(self):
@@ -124,13 +129,11 @@ class PostProcessor:
for process, datasets in self.processes["processes"].items():
parameters = (
- self.process_parameters[process].from_dict(
- self.process_parameters[process]
- )
- if process in self.parameters["processes"]["process_parameters"]
- else self.process_parameters[process].default()
+ self.parameters[process].from_dict(self.parameters[process])
+ if process in self.parameters["processes"]["parameters"]
+ else self.parameters[process].default()
)
- loaded_process = self.process_classfun[process](parameters)
+ loaded_process = self.classfun[process](parameters)
for dataset in datasets:
if isinstance(dataset, list): # multisignal process
signal = [self._signal[d] for d in dataset]
@@ -141,8 +144,8 @@ class PostProcessor:
result = loaded_process.run(signal)
- if process in self.parameters.to_dict()["process_outpaths"]:
- outpath = self.parameters.to_dict()["process_outpaths"][process]
+ if process in self.parameters.to_dict()["outpaths"]:
+ outpath = self.parameters.to_dict()["outpaths"][process]
elif isinstance(dataset, list):
# If no outpath defined, place the result in the minimum common
# branch of all signals used