ararpy 0.1.199__py3-none-any.whl → 0.2.2__py3-none-any.whl

ararpy/files/calc_file.py

@@ -22,7 +22,7 @@ import os
 import msoffcrypto
 
 from . import xls
-from ..calc.basic import get_datetime
+from ..calc.basic import get_datetime, parser
 from ..calc import arr, err, isochron
 
 
@@ -66,6 +66,7 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     data[-999] = [0] * data.index.size
     data[999] = [1] * data.index.size
     data[-1] = [np.nan] * data.index.size
+    data[-2] = [''] * data.index.size
     # rows_unm --> 样品阶段数
     sequence_index = [1, 2, ]
     sample_values_index = [16, 17, 21, 22, 26, 27, 31, 32, 36, 37,]
@@ -88,28 +89,27 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     isochron_values_index = [
         116, 117, 118, 119, 122,  # normal isochron
         -1, 127, 128, 129, 130, 133,  # inverse
-        -1, -999, -999, -999, -999, -999,  # 39/38 vs 40/38
-        -1, -999, -999, -999, -999, -999,  # 39/40 vs 39/40
-        -1, -999, -999, -999, -999, -999,  # 38/39 vs 40/39
-        -1, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 3D isochron, 36/39, 38/39, 40/39
+        -1, -1, -1, -1, -1, -1,  # 39/38 vs 40/38
+        -1, -1, -1, -1, -1, -1,  # 39/40 vs 39/40
+        -1, -1, -1, -1, -1, -1,  # 38/39 vs 40/39
+        -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 3D isochron, 36/39, 38/39, 40/39
     ]
     isochron_mark_index = [115,]
     total_param_index = [
         71, 72, 73, 74, 75, 76, 77, 78, 79, 80,  # 0-9
         81, 82, 83, 84, 85, 86, 87, 88, 89, 90,  # 10-19
-        91, 92, 93, 94, 95, 96, -999, -999, 63, -999,  # 20-29
-        -999, -999, -1, -1, -999, -999, -999, -999, -999, -999,  # 30-39
+        91, 92, 93, 94, 95, 96, -999, -2, 63, -999,  # 20-29
+        -999, -2, -1, -1, -999, -999, -999, -999, -999, -999,  # 30-39
         -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 40-49
         -999, -999, -999, -999, -999, -999, -999, -999, 67, 49,  # 50-59
         50, -999, -999, -999, -999, -999, -999, 51, 52, 53,  # 60-69
         54, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 70-79
         -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 80-89
-        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 90-99
-        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 100-109
-        -999, -999, -999, -999, -1,  # 110-114
-        -999, -999, -999, -999, -999, -999, -999, -999,  # 115-122
-        -999, -999, -999, -999, -999, -999, -999, -999,  # 123-130
-        -999, -999, -999, -999, -999,  # 131-135
+        -999, -999, -999, -999, -999, -999, -999, -2, -999, -999,  # 90-99
+        -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,  # 100-109
+        -2, -2, -2, -2, -2, -2, -999, -999, -999, -999,  # 110-119
+        -999, -999, -999, -999, -999, -999, 999, -999, 999, -999,  # 120-129
+        999, -999, 999, -999, 999, -999, 999, -999,  # 130-137
     ]
 
     # double transpose to remove keys
@@ -128,6 +128,14 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
 
     # adjustment
     isochron_mark.replace({4.0: '1'}, inplace=True)
+    isochron_mark.replace({'●': '1'}, inplace=True)
+
+    total_param[71] = 35.96754628
+    total_param[73] = 36.9667759
+    total_param[75] = 37.9627322
+    total_param[77] = 38.964313
+    total_param[79] = 39.962383123
+
     total_param[83] = logs01[1][9]  # No
     total_param[84] = logs01[1][10]  # %SD
     total_param[81] = logs01[1][11]  # K mass
@@ -150,9 +158,9 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     total_param[51] = logs01[1][27]  # %SD
     total_param[52] = logs01[1][28]  # 40K(\beta-) activities param
     total_param[53] = logs01[1][29]  # %SD
-    total_param[48] = logs01[1][26] + logs01[1][28]  # 40K(EC) activities param
-    total_param[49] = 100 / total_param[48] * pow(
-        (logs01[1][27] / 100 * logs01[1][26]) ** 2 + (logs01[1][29] / 100 * logs01[1][28]) ** 2, 0.5)  # %SD
+    total_param[48] = logs01[1][26] + logs01[1][28]  # 40K total activities param
+    total_param[49] = round(100 / total_param[48] * pow(
+        (logs01[1][27] / 100 * logs01[1][26]) ** 2 + (logs01[1][29] / 100 * logs01[1][28]) ** 2, 0.5), 6)  # %SD
 
     total_param[34] = logs01[1][36]  # decay constant of 40K total
     total_param[35] = logs01[1][37]  # %SD
@@ -169,30 +177,29 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     total_param[44] = logs01[1][40]  # decay constant of 37Ar
     total_param[45] = logs01[1][41]  # %SD
 
-    # logs01[1][49]]  # 1 for using weighted YORK isochron regression, 2 for unweighted
-    # logs01[1][50]]  # True for including errors on irradiation constants, False for excluding those
-    # [logs01[1][67]]  # MDF method, 'LIN'
+    # logs01[1][49]  # 1 for using weighted YORK isochron regression, 2 for unweighted
+    # logs01[1][50]  # True for including errors on irradiation constants, False for excluding those
+    # logs01[1][67]  # MDF method, 'LIN'
     total_param[93] = logs01[1][70]  # 40Ar/36Ar air
     total_param[94] = logs01[1][71]  # %SD
-
-    total_param[97] = 'York-2'  # Fitting method
+    total_param[97] = 'York-2' if int(logs01[1][49]) == 1 else ""   # Fitting method
     total_param[98] = logs01[1][0]  # Convergence
     total_param[99] = logs01[1][1]  # Iterations number
     total_param[100] = logs01[1][67]  # MDF method
-    total_param[101] = logs01[1][65]  # force negative to zero when correct blank
+    total_param[101] = parser(logs01[1][65], bool)  # force negative to zero when correct blank
     total_param[102] = True  # Apply 37Ar decay
     total_param[103] = True  # Apply 39Ar decay
-    total_param[104] = logs01[1][6]  # Apply 37Ar decay
-    total_param[105] = logs01[1][7]  # Apply 39Ar decay
-    total_param[106] = True  # Apply K degas
-    total_param[107] = True  # Apply Ca degas
-    total_param[108] = True  # Apply Air degas
-    total_param[109] = logs01[1][8]  # Apply Cl degas
+    total_param[104] = parser(logs01[1][6], bool)  # Apply 37Ar decay
+    total_param[105] = parser(logs01[1][7], bool)  # Apply 39Ar decay
+    total_param[106] = True  # Apply Ca degas
+    total_param[107] = True  # Apply K degas
+    total_param[108] = parser(logs01[1][8], bool)  # Apply Cl degas
+    total_param[109] = True  # Apply Trap degas
 
     total_param[110] = True if logs01[1][5] == 'MIN' else False  # Calculating ages using Min equation [True] or conventional equation [False]
-    total_param[111] = logs01[1][89]  # Use primary standard or not
-    total_param[112] = logs01[1][91]  # Use standard age or not
-    total_param[113] = logs01[1][92]  # Use primary ratio or not
+    total_param[111] = parser(logs01[1][89], bool)  # Use primary standard or not
+    total_param[112] = parser(logs01[1][91], bool)  # Use standard age or not
+    total_param[113] = parser(logs01[1][92], bool)  # Use primary ratio or not
 
     # irradiation time
     total_param = general_adjustment(
@@ -217,6 +224,7 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     data[-999] = [0] * data.index.size
     data[999] = [1] * data.index.size
     data[-1] = [np.nan] * data.index.size
+    data[-2] = [''] * data.index.size
     # values index
     sequence_index = [1, 2, ]
     sample_values_index = [16, 17, 21, 22, 26, 27, 31, 32, 36, 37,]
@@ -248,13 +256,13 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
         # inverse
         -1, 125, 126, 127, 128, 131,
         # 39/38 vs 40/38
-        -1, -999, -999, -999, -999, -999,
+        -1, -1, -1, -1, -1, -1,
         # 39/40 vs 39/40
-        -1, -999, -999, -999, -999, -999,
+        -1, -1, -1, -1, -1, -1,
         # 38/39 vs 40/39
-        -1, -999, -999, -999, -999, -999,
+        -1, -1, -1, -1, -1, -1,
         # 3D isochron, 36/39, 38/39, 40/39, r1, r2, r3
-        -1, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
     ]
     isochron_mark_index = [113,]
     total_param_index = [
@@ -286,8 +294,8 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
         -999, -999, -999, -999, -999, -999, -999, -999,
         # 123-130
         -999, -999, -999, -999, -999, -999, -999, -999,
-        # 131-135
-        -999, -999, -999, -999, -999,
+        # 131-137
+        -999, -999, -999, -999, -999, 999, -999,
     ]
 
     # double transpose to remove keys
@@ -310,12 +318,12 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     )
     # Do adjustment
     isochron_mark.replace({4.0: '1'}, inplace=True)
-    total_param[44] = logs01[1][40]
-    total_param[45] = logs01[1][41]
-    total_param[42] = logs01[1][38]
-    total_param[43] = logs01[1][39]
     total_param[34] = logs01[1][36]
     total_param[35] = logs01[1][37]
+    total_param[42] = logs01[1][38]
+    total_param[43] = logs01[1][39]
+    total_param[44] = logs01[1][40]
+    total_param[45] = logs01[1][41]
 
     return [
         sample_values, blank_values, corrected_values, degas_values, publish_values,
@@ -399,6 +407,8 @@ def general_adjustment(
     total_param[32] = [i / (3600 * 24 * 365.242) for i in stand_time_second]  # stand year
 
     # initial ratios & error display settings
+    total_param[95] = logs02[9][irradiation_index]  # 38Ar/36Ar air
+    total_param[96] = logs02[10][irradiation_index]  # %SD
     total_param[115] = 0
     total_param[116] = 298.56
     total_param[117] = 0.31
@@ -486,40 +496,41 @@ def open_full_xls(file_path: str, sample_name: str = ''):
         res['Inverse Isochron Table'], rows, [4, 5, 6, 7, 10])
     total_param = arr.partial(
         res['Sample Parameters'], rows, [
-            # 1, 2,  # 0-1
-            -1, -1, -1, -1,  # 2-5
-            -1, -1, -1, -1,  # 6-9
-            -1, -1, -1, -1, -1, -1,  # 10-15
-            -1, -1, -1, -1,  # 16-19
-            -1, -1,  # 20-21
-            23, 24, -1, -1, -1, -1,  # 22-27
-            -1, -1,  # 28-29
-            22, -1, -1, -1,  # 30-33
-            -1, -1,  # 34-35
-            -1, -1,  # 36-37
-            -1, -1,  # 38-39
-            -1, -1,  # 40-41
-            -1, -1,  # 42-43
-            -1, -1,  # 44-45
-            -1, -1,  # 46-47
-            -1, -1,  # 48-49
-            -1, -1,  # 50-51
-            -1, -1,  # 52-53
-            -1, -1,  # 54-55
-            -1, -1,  # 56-57
-            -1, -1,  # 58-59
-            -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 60-68
-            10, 11, 12, 13,  # 69-72
-            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 73-84
-            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 85-94
-            -1, -1, -1, -1,  # 95-98
-            -1, -1, -1, -1,  # 99-102
-            -1, -1, -1, -1,  # 103-106
-            -1, -1, -1, -1,  # 107-110
-            -1, -1, -1, -1,  # 111-114
-            -1, -1, -1, -1, -1, -1, -1, -1,  # 115-122
-            -1, -1, -1, -1, -1, -1, -1, -1,  # 123-130
-            -1, -1, -1, -1, -1,  # 131-135
+            # 1, 2, -1, # 0-2
+            -1, -1, -1, -1,  # 3-6
+            -1, -1, -1, -1,  # 7-10
+            -1, -1, -1, -1, -1, -1,  # 11-16
+            -1, -1, -1, -1,  # 17-20
+            -1, -1,  # 21-22
+            23, 24, -1, -1, -1, -1,  # 23-28
+            -1, -1,  # 29-30
+            22, -1, -1, -1,  # 31-34
+            -1, -1,  # 35-36
+            -1, -1,  # 37-38
+            -1, -1,  # 39-40
+            -1, -1,  # 41-42
+            -1, -1,  # 43-44
+            -1, -1,  # 45-46
+            -1, -1,  # 47-48
+            -1, -1,  # 49-50
+            -1, -1,  # 51-52
+            -1, -1,  # 53-54
+            -1, -1,  # 55-56
+            -1, -1,  # 57-58
+            -1, -1,  # 59-60
+            -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 61-69
+            10, 11, 12, 13,  # 70-73
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 74-85
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 86-95
+            -1, -1, -1, -1,  # 96-99
+            -1, -1, -1, -1,  # 100-103
+            -1, -1, -1, -1,  # 104-107
+            -1, -1, -1, -1,  # 108-111
+            -1, -1, -1, -1,  # 112-115
+            -1, -1, -1, -1, -1, -1, -1, -1,  # 116-123
+            -1, -1, -1, -1, -1, -1, -1, -1,  # 124-131
+            -1, -1, -1, -1, -1,  # 132-136
+            -1, -1, -1, -1,  # 137-140
         ])
 
     month_convert = {'Jan': '01', 'Feb': '02', 'Mar': '03', 'Apr': '04', 'May': '05', 'Jun': '06',
@@ -584,9 +595,9 @@ class ArArCalcFile:
         book_contents = read_calc_file(self.file_path)
         # create data frames for book values
         content = pd.DataFrame(book_contents['Data Tables'])
-        logs01 = pd.DataFrame(book_contents['Logs01'])
-        logs02 = pd.DataFrame(book_contents['Logs02'])
-        logs03 = pd.DataFrame(book_contents['Logs03'])
+        logs01 = pd.DataFrame(book_contents.get('Logs01', [[]]))
+        logs02 = pd.DataFrame(book_contents.get('Logs02', [[]]))
+        logs03 = pd.DataFrame(book_contents.get('Logs03', [[]]))
 
         start_row = 5
         sequence_num = int(logs03[2][0])
@@ -600,13 +611,15 @@ class ArArCalcFile:
         if version == '25.2':
             handler = open_252
             material = data[45][0]
+            irra_label = data[46][0]
             analyst = data[47][0]
         elif version == '24.0':
             handler = open_240
             material = data[46][0]
             analyst = data[48][0]
+            irra_label = ''
         else:
-            raise ValueError(f'non-supported version: {version}')
+            raise ValueError(f'Unsupported version: {version}')
 
         # change error type, 2sigma to 1sigma..., relative errors to absolute errors
         data = change_error_type(data, header)
@@ -624,15 +637,19 @@ class ArArCalcFile:
         # list(range(1, 26, 2)) irradiation correction constants
         # list(range(39, 58, 2)) decay constants
         # list(range(68, 97, 2)) J, MDF, other constants
-        for column in list(range(1, 26, 2)) + list(range(68, 71, 2)):
+        for column in list(range(1, 26, 2)) + list(range(68, 71, 2)):  # irradiation constants and J, MDF uncertainties
             self.content.loc[:, ('pam', column)] = \
-                (self.content['pam', column].astype("float") / (
-                    self.content['pam', column - 1].astype("float")) * 100).replace(np.nan, 0)
+                round(self.content['pam', column].astype("float") / (
+                    self.content['pam', column - 1].astype("float")) * 100, 6).replace(np.nan, 0)
 
         # sample info
         self.sample_info = {
+            'experiment': {
+                'name': self.sample_name,
+                'type': material, 'instrument': '', 'collectors': '','step_num': 0,
+            },
             'sample': {
-                'name': self.sample_name or data[44][0],
+                'name': data[44][0],
                 'material': material, 'location': 'LOCATION'
             },
             'researcher': {'name': data[64][0]},
@@ -640,7 +657,13 @@ class ArArCalcFile:
                 'name': logs01[1][44],
                 'analyst': analyst,
                 'info': '\n'.join([logs01[1][45], logs01[1][46], logs01[1][47]]),
-            }
+            },
+            'reference': {
+                'name': '', 'journal': '', 'doi': '',
+            },
+            'irradiation': {
+                'label': irra_label, 'pos_h': '', 'pos_x': '', 'pos_y': '',
+            },
         }
 
         return self