save_path2 attribute does not get set on preview run.

[daancs]

Hi!

Im trying to run SPACe on a small subset of the cpg0016-jump dataset (specifically cpg0016-jump/source_4/images/2021_04_26_Batch1/images/BR00117035__2021-05-02T16_02_51-Measurement1 from the AWS bucket).

I'm running a preview to see the segmentation on a few cells but am running into a problem in the SegmentationPartII class in the init function.

The self.save_path2.mkdir(exist_ok=True, parents=True) throws an error as the attribute save_path2 is null and never gets set on preview mode.

    if self.args.mode == "preview":
        self.load_path = self.args.main_path / self.args.experiment / f"Step0_MasksP1-Preview"
        self.save_path = self.args.main_path / self.args.experiment / f"Step0_MasksP2-Preview"
        self.num_workers = self.args.N
    else:
        self.load_path = self.args.main_path / self.args.experiment / f"Step{self.analysis_step-1}_MasksP1"
        self.save_path = self.args.main_path / self.args.experiment / f"Step{self.analysis_step}_MasksP2"
        self.save_path2 = self.args.main_path / self.args.experiment / f"Step{self.analysis_step}_MasksColor"
    self.save_path.mkdir(exist_ok=True, parents=True)
    self.save_path2.mkdir(exist_ok=True, parents=True)

I am unsure if this is intentional or if it is my fault but I can't get around this error on preview and won't be able to run the full pipeline due to insufficient computing power. Could use some insight here.