diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py index 57ff9cbefdeab4428cf4dba3393c95681141af7f..0e4bb3439298ba56ce15bbc9370a4ded95bc6d41 100644 --- a/model_server/extensions/chaeo/products.py +++ b/model_server/extensions/chaeo/products.py @@ -92,11 +92,6 @@ def get_patches_from_zmask_meta( focus_metric: str = None, **kwargs ) -> pd.DataFrame: - # patches = [] - - # for mi in zmask_meta: - # dfe = roiset.get_df().assign(patch=object()) - # for i, roi in enumerate(dfe.itertuples()): def _make_patch(roi): patch3d = roiset.acc_raw.data[roi.slice] @@ -161,41 +156,21 @@ def get_patches_from_zmask_meta( if pad_to: patch = pad(patch, pad_to) - - # patches.append(patch) return patch - # dfe.loc[i, 'patch'] = patch + dfe = roiset.get_df() dfe['patch'] = roiset.get_df().apply(lambda r: _make_patch(r), axis=1) return dfe - # if not make_3d and pc == 1: - # return MonoPatchStack(patches) - # else: - # return Multichannel3dPatchStack(patches) def export_patches_from_zstack( where: Path, - # stack: GenericImageDataAccessor, - # zmask_meta: list, roiset, - rescale_clip: float = 0.0, - pad_to: int = 256, - make_3d: bool = False, prefix='patch', - focus_metric: str = None, **kwargs ): - patches_df = get_patches_from_zmask_meta( - roiset, - # stack, - # zmask_meta, - # rescale_clip=rescale_clip, - pad_to=pad_to, - make_3d=make_3d, - focus_metric=focus_metric, - **kwargs - ) + make_3d = kwargs.get('make_3d', False) + patches_df = get_patches_from_zmask_meta(roiset, **kwargs) pc = roiset.acc_raw.chroma patches = list(patches_df['patch']) @@ -204,13 +179,8 @@ def export_patches_from_zstack( else: patches_acc = Multichannel3dPatchStack(patches) - exported = [] - for i, roi in enumerate(roiset.get_df().itertuples()): # just used for label info - # for i in range(0, len(zmask_meta)): - # mi = zmask_meta[i] + def _export_patch(roi): patch = patches_acc.iat_yxcz(i) - # obj = mi['info'] - # idx = mi['df_index'] ext = 'tif' if make_3d else 'png' fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}' @@ -223,6 +193,11 @@ def export_patches_from_zstack( 'df_index': roi.Index, 'patch_filename': fname, }) + + exported = [] + for i, roi in enumerate(patches_df.itertuples()): # just used for label info + _export_patch(roi) + return exported