continue implementing NexusEntry class

src/tavi/data/nxentry.py

@@ -115,14 +115,18 @@ def from_nexus(cls, path_to_nexus: str) -> dict:
             nexus_dict = NexusEntry._read_recursively(nexus_file)
         return cls([(key, val) for key, val in nexus_dict.items()])
 
-    def to_nexus(self, path_to_nexus: str) -> None:
+    # TODO
+    def to_nexus(self, path_to_nexus: str, name="scan") -> None:
         """write a NexueEntry instance to a NeXus file
 
         Args:
             path_to_nexus (str): path to a NeXus file with the extention .h5
         """
-        with h5py.File(path_to_nexus, "w") as nexus_file:
-            NexusEntry._write_recursively(self, nexus_file)
+        with h5py.File(path_to_nexus, "a") as nexus_file:
+            # TODO what if a group alreay exsit??
+            pass
+            scan_grp = nexus_file.create_group(name + "/")
+            NexusEntry._write_recursively(self, scan_grp)
 
     # TODO need to catch errors when multiple IPTS are loaded in a tavi file
     def get(self, key, ATTRS=False, default=None):

tests/test_nxentry.py

@@ -5,27 +5,33 @@
 from tavi.data.nxentry import NexusEntry
 
 
-def test_get_dataset(nexus_entry):
-    assert nexus_entry.get("definition") == "NXtas"
-    assert np.allclose(nexus_entry.get("a2"), np.array([242.0, 242.1, 242.2]))
-    assert nexus_entry.get("data", ATTRS=True) == {
+def test_get_dataset(nexus_entries):
+    scan0034 = nexus_entries["scan0034"]
+    assert scan0034.get("definition") == "NXtas"
+    assert scan0034.get("title") == "scan_title_34"
+    assert np.allclose(scan0034.get("a2"), np.array([242.0, 242.1, 242.2]))
+    assert scan0034.get("data", ATTRS=True) == {
         "EX_required": "true",
         "NX_class": "NXdata",
         "axes": "en",
         "signal": "detector",
     }
-    assert nexus_entry.get("a3") is None
-    assert nexus_entry.get("detector") is None
-    assert nexus_entry.get("detector/data", ATTRS=True) == {"EX_required": "true", "type": "NX_INT", "units": "counts"}
-    assert np.allclose(nexus_entry.get("instrument/analyser/a2"), np.array([242.0, 242.1, 242.2]))
+    assert scan0034.get("a3") is None
+    assert scan0034.get("detector") is None
+    assert scan0034.get("detector/data", ATTRS=True) == {"EX_required": "true", "type": "NX_INT", "units": "counts"}
+    assert np.allclose(scan0034.get("instrument/analyser/a2"), np.array([242.0, 242.1, 242.2]))
+
+    scan0035 = nexus_entries["scan0035"]
+    assert scan0035.get("title") == "scan_title_35"
 
 
-def test_to_nexus(nexus_entry):
+def test_to_nexus(nexus_entries):
     path_to_nexus_entry = "./test_data/scan_to_nexus_test.h5"
-    nexus_entry.to_nexus(path_to_nexus_entry)
+    for scan_num, nexus_entry in nexus_entries.items():
+        nexus_entry.to_nexus(path_to_nexus_entry, scan_num)
 
     with h5py.File(path_to_nexus_entry, "r") as nexus_file:
-        assert str(nexus_file["scan0034"]["title"].asstr()[...]) == "scan_title"
+        assert str(nexus_file["scan0034"]["title"].asstr()[...]) == "scan_title_34"
         assert nexus_file["scan0034"].attrs["NX_class"] == "NXentry"
 
 
@@ -56,42 +62,25 @@ def test_from_nexus_IPTS32124_CG4C_exp0424():
 
 
 @pytest.fixture
-def nexus_entry():
+def nexus_entries():
 
     analyser = {
-        "attrs": {
-            "EX_required": "true",
-            "NX_class": "NXcrystal",
-            "type": "NX_CHAR",
-        },
+        "attrs": {"EX_required": "true", "NX_class": "NXcrystal", "type": "NX_CHAR"},
         "a1": {
-            "attrs": {
-                "EX_required": "true",
-                "units": "degrees",
-            },
+            "attrs": {"EX_required": "true", "units": "degrees"},
             "dataset": np.array([142.0, 142.1, 142.2]),
         },
         "a2": {
-            "attrs": {
-                "EX_required": "true",
-                "units": "degrees",
-            },
+            "attrs": {"EX_required": "true", "units": "degrees"},
             "dataset": np.array([242.0, 242.1, 242.2]),
         },
         "sense": {"dataset": "-"},
         "type": {"dataset": "Pg002"},
     }
     detector = {
-        "attrs": {
-            "EX_required": "true",
-            "NX_class": "NXdetector",
-        },
+        "attrs": {"EX_required": "true", "NX_class": "NXdetector"},
         "data": {
-            "attrs": {
-                "EX_required": "true",
-                "type": "NX_INT",
-                "units": "counts",
-            },
+            "attrs": {"EX_required": "true", "type": "NX_INT", "units": "counts"},
         },
     }
 
@@ -101,10 +90,7 @@ def nexus_entry():
     }
     monitor = {
         "data": {
-            "attrs": {
-                "EX_required": "true",
-                "type": "NX_FLOAT",
-            },
+            "attrs": {"EX_required": "true", "type": "NX_FLOAT"},
             "dataset": np.array([60, 60, 60]),
         },
         "attrs": {
@@ -113,37 +99,45 @@ def nexus_entry():
         },
     }
 
-    nexus_entry = NexusEntry(
-        [
-            (
-                "scan0034",
-                {
-                    "attrs": {
-                        "EX_required": "true",
-                        "NX_class": "NXentry",
-                        "dataset_name": "IPTS32124_CG4C_exp0424",
-                    },
-                    "definition": {
-                        "attrs": {"EX_required": "true", "type": "NX_CHAR"},
-                        "dataset": "NXtas",
-                    },
-                    "title": {
-                        "attrs": {"EX_required": "true", "type": "NX_CHAR"},
-                        "dataset": "scan_title",
-                    },
-                    "data": {
-                        "attrs": {
-                            "EX_required": "true",
-                            "NX_class": "NXdata",
-                            "axes": "en",
-                            "signal": "detector",
-                        }
-                    },
-                    "instrument": instrument,
-                    "monitor": monitor,
-                },
-            )
-        ]
-    )
-
-    return nexus_entry
+    entries = {
+        # "scan0034": {
+        #     "attrs": {
+        #         "EX_required": "true",
+        #         "NX_class": "NXentry",
+        #         "dataset_name": "IPTS32124_CG4C_exp0424",
+        #     },
+        #     "definition": {
+        #         "attrs": {"EX_required": "true", "type": "NX_CHAR"},
+        #         "dataset": "NXtas",
+        #     },
+        #     "title": {
+        #         "attrs": {"EX_required": "true", "type": "NX_CHAR"},
+        #         "dataset": "scan_title_34",
+        #     },
+        #     "data": {
+        #         "attrs": {
+        #             "EX_required": "true",
+        #             "NX_class": "NXdata",
+        #             "axes": "en",
+        #             "signal": "detector",
+        #         }
+        #     },
+        #     "instrument": instrument,
+        #     "monitor": monitor,
+        # },
+        "scan0035": {
+            "title": {
+                "attrs": {"EX_required": "true", "type": "NX_CHAR"},
+                "dataset": "scan_title_35",
+            },
+        },
+    }
+
+    nexus_entres = {}
+    for scan_num, scan_content in entries.items():
+        content_list = []
+        for key, val in scan_content.items():
+            content_list.append((key, val))
+        nexus_entres.update({scan_num: NexusEntry(content_list)})
+
+    return nexus_entres