PyVisualFields 2.0.5__py3-none-any.whl → 2.0.7__py3-none-any.whl

PyVisualFields/Deviation_Analysis.py

@@ -803,19 +803,111 @@ def py_getgl(df_vf: pd.DataFrame) -> pd.DataFrame:
 
 #     return df_gp
 
+# def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
+#     """Global indices probability values."""
+
+#     nv = _nv()
+#     lut_dict = nv["glp_lut"]
+#     probs = nv["glp_probs"]
+#     idxm_0 = [i - 1 for i in (nv["glp_idxm"] or [])]
+#     idxs_0 = [i - 1 for i in (nv["glp_idxs"] or [])]
+
+#     gl_cols = ["msens", "ssens", "tmd", "tsd", "pmd", "psd", "gh", "vfi"]
+
+#     mean_cols = [gl_cols[i] for i in idxm_0 if i < len(gl_cols)]
+#     std_cols = [gl_cols[i] for i in idxs_0 if i < len(gl_cols)]
+
+#     n_probs = len(probs)
+
+#     prob_vals = np.array([
+#         _parse_lut_value(p) if isinstance(p, str) else float(p)
+#         for p in probs
+#     ])
+
+#     df_gp = df_gi.copy()
+
+#     def _prob_col_name(col):
+#         return f"{col}prob"
+
+#     def _build_col_lut(col):
+#         raw = lut_dict.get(col, [np.nan] * n_probs)
+#         return np.array([
+#             _parse_lut_value(v) if isinstance(v, str) else float(v)
+#             for v in raw
+#         ])
+
+#     # Left-tailed: lower values are abnormal
+#     for col in mean_cols:
+#         if col not in df_gi.columns:
+#             continue
+
+#         cutoffs = _build_col_lut(col)
+#         vals = df_gi[col].values.astype(float)
+#         vp = np.full(len(vals), np.nan)
+
+#         for i in range(n_probs - 1, 0, -1):
+#             vp[vals < cutoffs[i]] = prob_vals[i]
+
+#         df_gp[_prob_col_name(col)] = vp
+
+#     # Right-tailed: higher values are abnormal
+#     for col in std_cols:
+#         if col not in df_gi.columns:
+#             continue
+
+#         cutoffs = _build_col_lut(col)
+#         vals = df_gi[col].values.astype(float)
+#         vp = np.full(len(vals), np.nan)
+
+#         for i in range(n_probs - 1, 0, -1):
+#             vp[vals > cutoffs[i]] = prob_vals[i]
+
+#         df_gp[_prob_col_name(col)] = vp
+
+#     return df_gp
+
+
+
 def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
-    """Global indices probability values."""
+    """Compute missing global-index probability values only."""
 
     nv = _nv()
     lut_dict = nv["glp_lut"]
     probs = nv["glp_probs"]
+
     idxm_0 = [i - 1 for i in (nv["glp_idxm"] or [])]
     idxs_0 = [i - 1 for i in (nv["glp_idxs"] or [])]
 
     gl_cols = ["msens", "ssens", "tmd", "tsd", "pmd", "psd", "gh", "vfi"]
 
     mean_cols = [gl_cols[i] for i in idxm_0 if i < len(gl_cols)]
-    std_cols = [gl_cols[i] for i in idxs_0 if i < len(gl_cols)]
+    std_cols  = [gl_cols[i] for i in idxs_0 if i < len(gl_cols)]
+
+    def _prob_col_name(col):
+        return f"{col}prob"
+
+    # candidates that can be computed
+    computable_cols = [
+        c for c in (mean_cols + std_cols)
+        if c in df_gi.columns
+    ]
+
+    available_gl = [c for c in gl_cols if c in df_gi.columns]
+    missing_gl = [c for c in gl_cols if c not in df_gi.columns]
+
+    print(f"==> py_getglp: available globals: {available_gl}")
+    print(f"==> py_getglp: missing globals: {missing_gl}")
+
+    missing_prob_cols = [
+        c for c in computable_cols
+        if _prob_col_name(c) not in df_gi.columns
+    ]
+
+    print(f"==> py_getglp: missing global probability indices: "
+          f"{[_prob_col_name(c) for c in missing_prob_cols]}")
+
+    if not missing_prob_cols:
+        return df_gi.copy()
 
     n_probs = len(probs)
 
@@ -824,11 +916,6 @@ def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
         for p in probs
     ])
 
-    df_gp = df_gi.copy()
-
-    def _prob_col_name(col):
-        return f"{col}prob"
-
     def _build_col_lut(col):
         raw = lut_dict.get(col, [np.nan] * n_probs)
         return np.array([
@@ -836,9 +923,11 @@ def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
             for v in raw
         ])
 
+    computed = {}
+
     # Left-tailed: lower values are abnormal
     for col in mean_cols:
-        if col not in df_gi.columns:
+        if col not in missing_prob_cols:
             continue
 
         cutoffs = _build_col_lut(col)
@@ -848,11 +937,11 @@ def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
         for i in range(n_probs - 1, 0, -1):
             vp[vals < cutoffs[i]] = prob_vals[i]
 
-        df_gp[_prob_col_name(col)] = vp
+        computed[_prob_col_name(col)] = vp
 
     # Right-tailed: higher values are abnormal
     for col in std_cols:
-        if col not in df_gi.columns:
+        if col not in missing_prob_cols:
             continue
 
         cutoffs = _build_col_lut(col)
@@ -862,10 +951,27 @@ def py_getglp(df_gi: pd.DataFrame) -> pd.DataFrame:
         for i in range(n_probs - 1, 0, -1):
             vp[vals > cutoffs[i]] = prob_vals[i]
 
-        df_gp[_prob_col_name(col)] = vp
+        computed[_prob_col_name(col)] = vp
 
-    return df_gp
+    if "md" in df_gi.columns and "mdprob" not in df_gi.columns:
+        cutoffs = _build_col_lut("tmd")
+        vals = df_gi["md"].values.astype(float)
+        vp = np.full(len(vals), np.nan)
 
+        for i in range(n_probs - 1, 0, -1):
+            vp[vals < cutoffs[i]] = prob_vals[i]
+
+        computed["mdprob"] = vp
+
+    if computed:
+        out = pd.concat(
+            [df_gi.copy(), pd.DataFrame(computed, index=df_gi.index)],
+            axis=1,
+        )
+    else:
+        out = df_gi.copy()
+
+    return out
 
 def py_getallvalues(df_vf: pd.DataFrame):
     """Compute all deviations and global indices in one call.

PyVisualFields/PyGlaucoMetrics.py

@@ -311,11 +311,14 @@ def HAP2_part2_severity(row):
     l_cols = [f"l{i}" for i in range(1, 55) if f"l{i}" in row.index]
     pdp_cols = [f"pdp{i}" for i in range(1, 55) if f"pdp{i}" in row.index]
 
-    if "md" not in row.index:
-        return "Unknown"
+    # if "md" not in row.index:
+    #     return "Unknown"
 
-    md = pd.to_numeric(row["md"], errors="coerce")
-    if pd.isna(md):
+    if "md" in row.index and pd.notna(row["md"]):
+        md = pd.to_numeric(row["md"], errors="coerce")
+    elif "tmd" in row.index and pd.notna(row["tmd"]):
+        md = pd.to_numeric(row["tmd"], errors="coerce")
+    else:
         return "Unknown"
 
     sens = pd.to_numeric(row[l_cols], errors="coerce")
@@ -371,9 +374,25 @@ def HAP2_part2_severity(row):
         return "Early"
 
     # -------------------------
-    # Otherwise moderate
+    # Moderate defect
+    # At least one criterion
     # -------------------------
-    return "Moderate"
+    only_one_hemifield_central_lt15 = (
+        (sup_lt15 and not inf_lt15)
+        or (inf_lt15 and not sup_lt15)
+    )
+
+    moderate = (
+        (-12 <= md <= -6)
+        or (only_one_hemifield_central_lt15 and not any_central_0)
+        or (13 <= n_pdp_5 <= 26)
+        or (5 <= n_pdp_1 <= 13)
+    )
+
+    if moderate:
+        return "Moderate"
+
+    return ""
 
 
 def Fn_HAP2_part2(df):

PyVisualFields/__init__.py

@@ -1 +1 @@
-__version__ = "2.0.5"
+__version__ = "2.0.7"

PyVisualFields/utils.py

@@ -119,34 +119,62 @@ META_ALIASES = {
     "vfi": [
         "vfi"
     ],
+    #probability
+    "vfiprob": [
+        "vfi_p", "vfiprob", "vfip"
+    ],
 
     "msens": [
         "msens", "ms", "meansensitivity"
     ],
+    #probability
+    "msensprob": [
+        "msens_p", "msensprob", "msenp", "ms_p", "msprob", "msp"
+    ],
 
     "ssens": [
         "ssens", "ss", "sdsensitivity"
     ],
+    #probability
+    "ssensprob": [
+        "ssens_p", "ssensprob", "lsenp", "ss_p", "ssprob", "ssp"
+    ],
 
     "tmd": [
         "tmd"
     ],
+    #probability
+    "tmdprob": [
+        "tmd_p", "tmdprob", "tmdp"
+    ],
 
     "tsd": [
         "tsd"
     ],
+    #probability
+    "tsdprob": [
+        "tsd_p", "tsdprob", "tsdp"
+    ],
 
     "pmd": [
         "pmd"
     ],
+    #probability
+    "pmdprob": [
+        "pmd_p", "pmdprob", "pmdp"
+    ],
 
     "gh": [
         "gh", "generalheight"
     ],
+    #probability
+    "ghprob": [
+        "gh_p", "ghprob", "ghp"
+    ],
 
     # Reliability
     "fpr": [
-        "fpr"
+        "fpr" 
     ],
 
     "fnr": [

{pyvisualfields-2.0.5.dist-info → pyvisualfields-2.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyVisualFields
-Version: 2.0.5
+Version: 2.0.7
 Summary: A python toolkit for visual field analysis
 Home-page: https://github.com/mohaEs/PyVisualField
 Author: Mohammad Eslami, Bharath Erusalagandi, Mousa Moradi

{pyvisualfields-2.0.5.dist-info → pyvisualfields-2.0.7.dist-info}/RECORD

@@ -1,7 +1,7 @@
-PyVisualFields/Deviation_Analysis.py,sha256=kgi0fJyF0wvJTDjswiD6F7DC78S0s4B1Siu8By3IjzA,28110
-PyVisualFields/PyGlaucoMetrics.py,sha256=SGKiihats2IU3sME3GdYyg2933U-sb7Jk1NwXzE6lCA,23432
-PyVisualFields/__init__.py,sha256=xEb7Z4b8xalXXExBg42XPAhbJKniHzcsEPjp-6S3ppg,22
-PyVisualFields/utils.py,sha256=z_jnJiLnbxTH1hkN-ZfVNmCQqpJwsuYXSl0wEYx7uRE,24626
+PyVisualFields/Deviation_Analysis.py,sha256=KR8m73JMDDYjbj5cDEyxTFbMiyNp0C8Xy5nVTbLXQqw,31152
+PyVisualFields/PyGlaucoMetrics.py,sha256=-Uj_pO9yxqY6-H4ZhrSRdE3zbMdnyy68wLo2i_kmvN0,23956
+PyVisualFields/__init__.py,sha256=L4aOgvDE9n_eqL_mM_j5bO3bQ73q6ulNpnVuG8OmqWE,22
+PyVisualFields/utils.py,sha256=sYZOqnd5kIimbZh8u0sj89pFXx6SYId5rESg_BO6AsA,25219
 PyVisualFields/vfprogression.py,sha256=FjKtVZ3DRcS31CZRcAHMTfDxYYF3UWLTOjcr3YZdCRg,34215
 PyVisualFields/visualFields.py,sha256=aSZaKE5pc67TyuVtrMLYtKe7lbInzVWKnpP-6ezQwHA,61905
 PyVisualFields/pkl_files/locmaps.json,sha256=VQ8L0DvBG8GouJD_ZsgQa8O1SteDMFPFTSPaW8TgL7c,1694
@@ -18,8 +18,8 @@ PyVisualFields/pkl_files/vfctrSunyiu24d2.pkl,sha256=e2hspPbpVYWXBDVn6fJ9KRK-JYIH
 PyVisualFields/pkl_files/vfpwgRetest24d2.pkl,sha256=WyWZ3mHr1JL4TCUVUu0WFpIFdqAiwvNyL_pd51duPKY,106683
 PyVisualFields/pkl_files/vfpwgSunyiu24d2.pkl,sha256=kYIreVpqaRX-Hkl9ZPZ7agnqJplu8DxFM08X17L_fTg,14598
 PyVisualFields/pkl_files/vfseries.pkl,sha256=aWkDkByTkgmCKH2nYZrB1hoHt-fi_FxY1gamZ6iqZu0,36363
-pyvisualfields-2.0.5.dist-info/licenses/LICENSE,sha256=m3BJDRLy-Xnz1WmgtnVniIpPIlwv0MYil80-tjCetYc,1570
-pyvisualfields-2.0.5.dist-info/METADATA,sha256=VhfsyRalJs45ipPdWCtRQpx_eFlAmKefEkGotgo-Ths,12829
-pyvisualfields-2.0.5.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-pyvisualfields-2.0.5.dist-info/top_level.txt,sha256=r-Mpr1QBoJaRDJQ-POzcuukSnBCkNasixPj3P2UWWRw,15
-pyvisualfields-2.0.5.dist-info/RECORD,,
+pyvisualfields-2.0.7.dist-info/licenses/LICENSE,sha256=m3BJDRLy-Xnz1WmgtnVniIpPIlwv0MYil80-tjCetYc,1570
+pyvisualfields-2.0.7.dist-info/METADATA,sha256=7G6xPj_WBWENM1XJSfBga1IC3-Jpg29Af5M5FWbpOYQ,12829
+pyvisualfields-2.0.7.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+pyvisualfields-2.0.7.dist-info/top_level.txt,sha256=r-Mpr1QBoJaRDJQ-POzcuukSnBCkNasixPj3P2UWWRw,15
+pyvisualfields-2.0.7.dist-info/RECORD,,