diff --git a/src/wela/dataloader.py b/src/wela/dataloader.py index f19a8e0c1ef9a7a74bd7fb3ff66d82fb25916cb5..44570b4414f0452df94a5f25eee547e86ca681e2 100644 --- a/src/wela/dataloader.py +++ b/src/wela/dataloader.py @@ -76,40 +76,49 @@ class dataloader: def __init__(self, h5dir=None, wdir=".", ls=True): # from grouper.signals to abbreviations - self.g2a_dict = { + self.g2a_dict = self.define_g2a_dict() + # from abbreviations to grouper.siglist + self.a2g_dict = {v: k for (k, v) in self.g2a_dict.items()} + # establish paths + self.wdirpath = Path(wdir) + if h5dir is None: + self.h5dirpath = None + else: + self.h5dirpath = Path(h5dir) + if ls: + self.ls + + def define_g2a_dict(self): + """Dict to convert names of grouper.signals to short forms.""" + g2a_dict = { "extraction/cy5/max/median": "cy5", "extraction/general/None/area": "area", "extraction/general/None/volume": "volume", + "extraction/general/None/image_x": "image_x", + "extraction/general/None/image_y": "image_y", + "extraction/general/None/absolute_x": "absolute_x", + "extraction/general/None/absolute_y": "absolute_y", "extraction/Flavin_bgsub/max/mean": "flavin", "postprocessing/buddings/extraction_general_None_volume": "buddings", "postprocessing/bud_metric/extraction_general_None_volume": "bud_volume", } for fl in ["GFP", "mCherry"]: - self.g2a_dict[f"extraction/{fl}/max/median"] = f"median_{fl}" - self.g2a_dict[f"extraction/{fl}/max/mean"] = f"mean_{fl}" - self.g2a_dict[f"extraction/{fl}/max/std"] = f"std_{fl}" - self.g2a_dict[f"extraction/{fl}/max/max5px_median"] = ( + g2a_dict[f"extraction/{fl}/max/median"] = f"median_{fl}" + g2a_dict[f"extraction/{fl}/max/mean"] = f"mean_{fl}" + g2a_dict[f"extraction/{fl}/max/std"] = f"std_{fl}" + g2a_dict[f"extraction/{fl}/max/max5px_median"] = ( f"max5px_median_{fl}" ) - self.g2a_dict[ + g2a_dict[ f"postprocessing/bud_metric/extraction_{fl}_max_median" ] = f"bud_median_{fl}" - self.g2a_dict[ - f"postprocessing/bud_metric/extraction_{fl}_max_mean" - ] = f"bud_mean_{fl}" - self.g2a_dict[ - f"postprocessing/bud_metric/extraction_{fl}_max_std" - ] = f"bud_std_{fl}" - # from abbreviations to grouper.siglist - self.a2g_dict = {v: k for (k, v) in self.g2a_dict.items()} - # establish paths - self.wdirpath = Path(wdir) - if h5dir is None: - self.h5dirpath = None - else: - self.h5dirpath = Path(h5dir) - if ls: - self.ls + g2a_dict[f"postprocessing/bud_metric/extraction_{fl}_max_mean"] = ( + f"bud_mean_{fl}" + ) + g2a_dict[f"postprocessing/bud_metric/extraction_{fl}_max_std"] = ( + f"bud_std_{fl}" + ) + return g2a_dict @property def ls(self): @@ -283,7 +292,7 @@ class dataloader: print(" ", signal) print() if self.a2g_dict[key_index] not in grouper.available: - raise Exception(f"the key index {key_index} is unavailable.") + raise Exception(f"The key index {key_index} is unavailable.") # get indices for all buds bud_indices = self.get_bud_indices(grouper, key_index) # get key_index data