changed ptycho/ to class/methods.

TODO: also change bo/, fix main.py

ptycho/ptycho_example.py

@@ -0,0 +1,41 @@
+from typing import Any
+from ptycho.ptycho_base import PtychoEngine
+
+class ExamplePtychoEngine(PtychoEngine):
+
+    # initialize job/engine-specific variables here
+    # e.g. self.output_dir
+    
+    def __init__(self, config):
+        super().__init__(config)
+
+    # run single ptychography job based on `config`
+    def run(self) -> None:
+        pass
+    
+    # save outputs to self._output
+    def output(self) -> Any:
+        if self._output is None:
+            pass
+        return self._output
+    
+    # return reconstructed object (numpy array)
+    def recon_object(self) -> Any:
+        if self._recon_object is None:
+            output = self.output()
+            pass
+        return self._recon_object
+
+    # return reconstructed probe (numpy array)
+    def recon_probe(self) -> Any:
+        if self._recon_probe is None:
+            output = self.output()
+            pass
+        return self._recon_probe
+    
+    # return metric value for Bayesian optimization
+    def metric(self) -> float:
+        if self._metric is None:
+            output = self.output()
+            self._metric = 0.0
+        return self._metric