Source code for cryocare.protocols.protocol_load_model


from pwem.protocols import EMProtocol
from pyworkflow.protocol import PathParam, FileParam
from pyworkflow.utils import Message
from cryocare.objects import CryocareModel


[docs]class ProtCryoCARELoadModel(EMProtocol): """Use two data-independent reconstructed tomograms to train a 3D cryo-CARE network.""" _label = 'CryoCARE Load Model' # -------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): """ Define the input parameters that will be used. Params: form: this is the form to be populated with sections and params. """ # You need a params to belong to a section: form.addSection(label=Message.LABEL_INPUT) form.addParam('basedir', PathParam, label='Basedir', important=True, allowsNull=False, help='Base directory of the trained cryoCARE model.') form.addParam('meanStd', FileParam, label='Normalization file (mean_std)', important=True, allowsNull=False, help='mean_std.npz file generated when preparing the training data.') def _insertAllSteps(self): self._insertFunctionStep('createOutputStep')
[docs] def createOutputStep(self): model = CryocareModel(basedir=self.basedir.get(), mean_std=self.meanStd.get()) self._defineOutputs(model=model)
# --------------------------- INFO functions ----------------------------------- def _summary(self): summary = [] if self.isFinished(): summary.append("Loaded training model info:\n" "model_dir = *{}*\n" "normalization_file = *{}*".format (self.basedir.get(), self.meanStd.get())) return summary