Added ingest methods to move experimental data to aimmdb

.pre-commit-config.yaml

@@ -13,17 +13,17 @@ repos:
     -   id: check-yaml
     -   id: debug-statements
 
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 4.0.1
+-   repo: https://github.com/pycqa/flake8
+    rev: 7.1.0
     hooks:
     -   id: flake8
 
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.9.3
+    rev: 5.13.2
     hooks:
     -   id: isort
 
 -   repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 24.4.2
     hooks:
     -   id: black

aimm_adapters/aimm_elecrochem.py

@@ -0,0 +1,101 @@
+import pathlib
+import re
+
+import pandas as pd
+
+
+def parse_charge(charge_params):
+    if "C" in charge_params:
+        state = "C"
+    else:
+        state = "DC"
+
+    cycle = int(charge_params[:-1])
+
+    charge = {"cycle": cycle, "state": state}
+
+    return charge
+
+
+def read_electrochem(c, data_path):
+    c_uid = c["uid"]
+
+    files = list(data_path.glob("*.csv"))
+
+    data = []
+    metadata = []
+
+    extra_meta = {
+        "NCM622": {"loading_mass": 0.1638, "current": 30},
+        "NCM712": {"loading_mass": 0.1661, "current": 30},
+        "NCM712-Al": {"loading_mass": 0.1568, "current": 30},
+        "NCM811": {"loading_mass": 0.1675, "current": 30},
+        "NCMA": {"loading_mass": 0.1671, "current": 30},
+    }
+
+    units = {"units": {"loading_mass": "g", "current": "mA/g"}}
+
+    for file in files:
+        fname = file.name
+        print(fname)
+
+        if file.stem == "811-Al":
+            sample_name = "NCMA"
+        else:
+            sample_name = "NCM" + file.stem
+
+        with open(file, "r") as f:
+            raw_df = pd.read_csv(f, sep=",", header=[0, 1])
+
+            for i in range(0, raw_df.shape[1], 2):
+                columns = [
+                    raw_df.iloc[:, i].name[0],
+                    raw_df.iloc[:, i + 1].name[0],
+                ]  # To save in the metadata
+                edited_columns = [
+                    columns[0].split()[0].lower(),
+                    columns[1].split()[0].lower(),
+                ]  # No units; just the names.
+                # To use in the dataframes used in tiled
+                table_units = {
+                    edited_columns[0]: re.sub("[()]", "", columns[0].split()[1]),
+                    edited_columns[1]: re.sub("[()]", "", columns[1].split()[1]),
+                }
+
+                df = pd.DataFrame(
+                    {
+                        edited_columns[0]: raw_df.iloc[:, i],
+                        edited_columns[1]: raw_df.iloc[:, i + 1],
+                    }
+                )
+                df = df.dropna()
+
+                charge = parse_charge(raw_df.iloc[:, i].name[1])
+                meta = {
+                    "dataset": "nmc_electrochem",
+                    "fname": fname,
+                    "facility": {"name": "ALS"},
+                    "beamline": {"name": "8.0.1"},
+                    "sample": {"name": sample_name},
+                    "charge": charge,
+                }
+
+                meta.update(extra_meta[sample_name])
+                meta.update(units)
+                meta["units"].update(table_units)
+
+                c_uid.write_dataframe(df, meta, specs=["electrochemistry"])
+
+                data.append(df)
+                metadata.append(meta)
+
+    return data, metadata
+
+
+if __name__ == "__main__":
+
+    data_path = pathlib.Path(
+        "C:/Users/jmaruland/Documents/GitHub/aimm-adapters/aimm_adapters/files"
+    )
+
+    data, metadata = read_electrochem(data_path)