kardioutils 1.0.18__tar.gz → 1.0.19__tar.gz

{kardioutils-1.0.18/kardioutils.egg-info → kardioutils-1.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kardioutils
-Version: 1.0.18
+Version: 1.0.19
 Summary: Utils lib
 Author: João Neto
 Author-email: joao.filipe.neto@gmail.com

kardioutils-1.0.19/dl2050utils/__version__.py

@@ -0,0 +1 @@
+version = "1.0.19"

{kardioutils-1.0.18 → kardioutils-1.0.19}/dl2050utils/db.py

@@ -749,8 +749,10 @@ def db_import_tbl(db, p, tbl, delete=False):
     if rows is None:
         return log_and_return(f"Cant read {p}")
     if delete:
-        if db.sync_execute(f"delete from {tbl}"):
+        res = db.sync_execute(f"DELETE FROM {tbl}")
+        if res is None:
             return log_and_return(f"Error deleting tbl {tbl}")
+        print("Delete result:", res) 
     n = 0
     for row in rows:
         res = db.sync_insert(tbl, row)

kardioutils-1.0.19/dl2050utils/df_utils.py

@@ -0,0 +1,155 @@
+import pandas as pd
+import os
+from __future__ import annotations
+from typing import Tuple, List, Optional
+import numpy as np
+
+def list_prefixes(df: pd.DataFrame) -> list:
+    """Return all distinct prefixes in the dataframe."""
+    return df["prefix"].dropna().unique().tolist()
+
+
+def filter_by_prefix(df: pd.DataFrame, prefix: str) -> pd.DataFrame:
+    """Return all rows that match a given prefix exactly."""
+    return df[df["prefix"] == prefix]
+
+
+def filter_prefix_contains(df: pd.DataFrame, text: str) -> pd.DataFrame:
+    """Return all rows where prefix contains the given text."""
+    return df[df["prefix"].str.contains(text, na=False)]
+
+
+def find_by_uid_suffix(df: pd.DataFrame, uid_suffix: str) -> pd.DataFrame:
+    """Return all rows that match a given uid_suffix."""
+    return df[df["uid_suffix"] == uid_suffix]
+
+
+def find_by_uid_full(df: pd.DataFrame, uid_full: str) -> pd.DataFrame:
+    """Return all rows that match a given uid_full."""
+    return df[df["uid_full"] == uid_full]
+
+
+def holter_only(df: pd.DataFrame) -> pd.DataFrame:
+    """Return only rows where holter == True."""
+    return df[df["holter"] == True]
+
+
+def non_holter_only(df: pd.DataFrame) -> pd.DataFrame:
+    """Return only rows where holter == False."""
+    return df[df["holter"] == False]
+
+
+def get_path_by_uid_suffix(df: pd.DataFrame, uid_suffix: str) -> str | None:
+    """
+    Return the path for a given uid_suffix.
+    If there are multiple rows, returns the first one.
+    If nothing is found, returns None.
+    """
+    rows = df[df["uid_suffix"] == uid_suffix]
+    if rows.empty:
+        return None
+    return rows.iloc[0]["path"]
+
+
+def get_paths_by_prefix(df: pd.DataFrame, prefix: str, holter_only_flag: bool | None = None) -> list:
+    """
+    Return a list of paths filtered by prefix and optionally holter flag.
+    - holter_only_flag = True  → only holter rows
+    - holter_only_flag = False → only non-holter rows
+    - holter_only_flag = None  → ignore holter column
+    """
+    subset = df[df["prefix"] == prefix]
+    if holter_only_flag is not None:
+        subset = subset[subset["holter"] == holter_only_flag]
+    return subset["path"].dropna().tolist()
+
+
+def check_missing_files(df):
+    """
+    Return subset of rows whose 'path' does not point to an existing file.
+    """
+    mask = ~df["path"].astype(str).apply(os.path.exists)
+    return df[mask]
+
+
+def check_existing_files(df):
+    """
+    Return subset of rows whose 'path' exists.
+    """
+    mask = df["path"].astype(str).apply(os.path.exists)
+    return df[mask]
+
+def load_X_from_index_df(
+    index_df: pd.DataFrame,
+    fdb,
+    *,
+    uid_col: str = "uid_full",
+    pre: str = "x_",
+    ext: str = ".npy",
+    allow_pickle: bool = False,
+    stack: bool = True,
+    on_missing: str = "skip",   # "skip" | "raise" | "keep_none"
+) -> Tuple[np.ndarray, List[str], pd.DataFrame]:
+    """
+    Loads x_ arrays for each row in index_df using fdb.load(row[uid_col], pre, ext).
+
+    Returns:
+      - X: stacked np.ndarray (N, ...) if stack=True; otherwise object array of length N
+      - ids: list of ids in the same order as X
+      - meta: dataframe aligned with X (rows kept), including a 'loaded' boolean column
+    """
+    if uid_col not in index_df.columns:
+        raise KeyError(f"uid_col '{uid_col}' not found in index_df columns")
+
+    loaded_arrays = []
+    kept_ids: List[str] = []
+    kept_rows = []
+    missing_rows = []
+
+    for _, row in index_df.iterrows():
+        uid = row[uid_col]
+        arr = fdb.load(uid, pre=pre, ext=ext, allow_pickle=allow_pickle)
+
+        if arr is None:
+            if on_missing == "raise":
+                raise FileNotFoundError(f"Missing array for {uid} (pre={pre}, ext={ext})")
+            if on_missing == "keep_none":
+                loaded_arrays.append(None)
+                kept_ids.append(uid)
+                r = row.copy()
+                r["loaded"] = False
+                kept_rows.append(r)
+            else:  # skip
+                r = row.copy()
+                r["loaded"] = False
+                missing_rows.append(r)
+            continue
+
+        loaded_arrays.append(arr)
+        kept_ids.append(uid)
+        r = row.copy()
+        r["loaded"] = True
+        kept_rows.append(r)
+
+    meta = pd.DataFrame(kept_rows).reset_index(drop=True)
+
+    if not stack:
+        # keep as object array (useful if shapes can differ or you used keep_none)
+        X = np.array(loaded_arrays, dtype=object)
+        return X, kept_ids, meta
+
+    # stack=True: require all arrays exist and have same shape
+    arrays_only = [a for a in loaded_arrays if a is not None]
+    if len(arrays_only) == 0:
+        return np.empty((0,), dtype=float), kept_ids, meta
+
+    try:
+        X = np.stack(arrays_only, axis=0)
+    except Exception as e:
+        raise ValueError(
+            "Could not stack arrays (shapes likely differ). "
+            "Use stack=False or handle padding/truncation."
+        ) from e
+
+   
+    return X, kept_ids, meta

{kardioutils-1.0.18 → kardioutils-1.0.19/kardioutils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kardioutils
-Version: 1.0.18
+Version: 1.0.19
 Summary: Utils lib
 Author: João Neto
 Author-email: joao.filipe.neto@gmail.com

kardioutils-1.0.18/dl2050utils/__version__.py

@@ -1 +0,0 @@
-version = "1.0.18"

kardioutils-1.0.18/dl2050utils/df_utils.py

@@ -1,77 +0,0 @@
-import pandas as pd
-import os
-
-def list_prefixes(df: pd.DataFrame) -> list:
-    """Return all distinct prefixes in the dataframe."""
-    return df["prefix"].dropna().unique().tolist()
-
-
-def filter_by_prefix(df: pd.DataFrame, prefix: str) -> pd.DataFrame:
-    """Return all rows that match a given prefix exactly."""
-    return df[df["prefix"] == prefix]
-
-
-def filter_prefix_contains(df: pd.DataFrame, text: str) -> pd.DataFrame:
-    """Return all rows where prefix contains the given text."""
-    return df[df["prefix"].str.contains(text, na=False)]
-
-
-def find_by_uid_suffix(df: pd.DataFrame, uid_suffix: str) -> pd.DataFrame:
-    """Return all rows that match a given uid_suffix."""
-    return df[df["uid_suffix"] == uid_suffix]
-
-
-def find_by_uid_full(df: pd.DataFrame, uid_full: str) -> pd.DataFrame:
-    """Return all rows that match a given uid_full."""
-    return df[df["uid_full"] == uid_full]
-
-
-def holter_only(df: pd.DataFrame) -> pd.DataFrame:
-    """Return only rows where holter == True."""
-    return df[df["holter"] == True]
-
-
-def non_holter_only(df: pd.DataFrame) -> pd.DataFrame:
-    """Return only rows where holter == False."""
-    return df[df["holter"] == False]
-
-
-def get_path_by_uid_suffix(df: pd.DataFrame, uid_suffix: str) -> str | None:
-    """
-    Return the path for a given uid_suffix.
-    If there are multiple rows, returns the first one.
-    If nothing is found, returns None.
-    """
-    rows = df[df["uid_suffix"] == uid_suffix]
-    if rows.empty:
-        return None
-    return rows.iloc[0]["path"]
-
-
-def get_paths_by_prefix(df: pd.DataFrame, prefix: str, holter_only_flag: bool | None = None) -> list:
-    """
-    Return a list of paths filtered by prefix and optionally holter flag.
-    - holter_only_flag = True  → only holter rows
-    - holter_only_flag = False → only non-holter rows
-    - holter_only_flag = None  → ignore holter column
-    """
-    subset = df[df["prefix"] == prefix]
-    if holter_only_flag is not None:
-        subset = subset[subset["holter"] == holter_only_flag]
-    return subset["path"].dropna().tolist()
-
-
-def check_missing_files(df):
-    """
-    Return subset of rows whose 'path' does not point to an existing file.
-    """
-    mask = ~df["path"].astype(str).apply(os.path.exists)
-    return df[mask]
-
-
-def check_existing_files(df):
-    """
-    Return subset of rows whose 'path' exists.
-    """
-    mask = df["path"].astype(str).apply(os.path.exists)
-    return df[mask]