♻️ rename to acq2sqlite.py

01_txt_to_sqlite.bash

@@ -0,0 +1 @@
+./acq2sqlite.py

01_txt_to_sqlite.py → acq2sqlite.py

@@ -27,7 +27,6 @@ def column_names():
 
 
 COLNAMES = column_names()
-sql = sqlite3.connect("db.sqlite")  # see schema.sql
 
 ### SQL queries
 # These are the header values (now sql columns) that should be consistant for an acquistion ('SequenceName') in a specific study ('Project')
@@ -57,7 +56,7 @@ def column_names():
 
 # otherwise we'll need to create a new row
 consts_ins_string = ",".join(CONSTS)
-val_quests = ",".join(["?" for k in CONSTS])
+val_quests = ",".join(["?" for _ in CONSTS])
 sql_cmd = f"INSERT INTO acq_param({consts_ins_string}) VALUES({val_quests});"
 
 ## we'll do the same thing for the acquisition paramaters (e.g. time and series number) that change very time -- only add if not already in the DB
@@ -72,33 +71,42 @@ def column_names():
 acq_insert = f"INSERT INTO acq({','.join(acq_insert_columns)}) VALUES({','.join(['?' for _ in acq_insert_columns])});"
 
 
-with open("db.txt", "r") as f:
-    while line := f.readline():
-        vals = line.split("\t")
-        d = dict(zip(COLNAMES, vals))
-        # order here needs to match find_acq.
-        acq_search_vals = (d["AcqTime"], d["AcqDate"], d["SubID"], d["SeriesNumber"])
-        cur = sql.execute(find_acq, acq_search_vals)
-        acq = cur.fetchone()
-        if acq:
-            print(f"have acq {acq[0]} {acq_search_vals}")
-            continue
-
-        val_array = [d[k] for k in CONSTS]
-        print(f"searching: {val_array}")
-        cur = sql.execute(find_cmd, val_array)
-        res = cur.fetchone()
-        if res:
-            rowid = res[0]
-            print(f"seq repeated: found exiting {rowid}")
-        else:
-            cur = sql.execute(sql_cmd, val_array)
-            rowid = cur.lastrowid
-            print(f"new seq: created {rowid}")
-        ###
-        d["param_id"] = rowid
-        acq_insert_vals = [d[k] for k in acq_insert_columns]
-        cur = sql.execute(acq_insert, acq_insert_vals)
-        print(f"new acq: created {cur.lastrowid}")
-
-sql.commit()
+def dict_to_db_row(d, sql):
+    """
+    insert a dicom header (representive of acquistion) into db
+    """
+    # order here needs to match find_acq.
+    acq_search_vals = (d["AcqTime"], d["AcqDate"], d["SubID"], d["SeriesNumber"])
+    cur = sql.execute(find_acq, acq_search_vals)
+    acq = cur.fetchone()
+    if acq:
+        print(f"have acq {acq[0]} {acq_search_vals}")
+        return
+
+    val_array = [d[k] for k in CONSTS]
+    print(f"searching: {val_array}")
+    cur = sql.execute(find_cmd, val_array)
+    res = cur.fetchone()
+    if res:
+        rowid = res[0]
+        print(f"seq repeated: found exiting {rowid}")
+    else:
+        cur = sql.execute(sql_cmd, val_array)
+        rowid = cur.lastrowid
+        print(f"new seq: created {rowid}")
+    ###
+    d["param_id"] = rowid
+    acq_insert_vals = [d[k] for k in acq_insert_columns]
+    cur = sql.execute(acq_insert, acq_insert_vals)
+    print(f"new acq: created {cur.lastrowid}")
+
+
+if __name__ == "__main__":
+    sql = sqlite3.connect("db.sqlite")  # see schema.sql
+    with open("db.txt", "r") as f:
+        while line := f.readline():
+            vals = line.split("\t")
+            d = dict(zip(COLNAMES, vals))
+            dict_to_db_row(d, sql)
+
+    sql.commit()

sphinx/index.rst

@@ -18,4 +18,4 @@ Code to parse dicoms into a template database and alert on non-conforming sequen
 
    change_header
    dcmmeta2tsv
-   01_txt_to_sqlite
+   acq2sqlite