pymast 0.0.5__py3-none-any.whl → 1.0.0__py3-none-any.whl

pymast/table_merge.py

@@ -1,154 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Modules contains all of the functions to merge individual radio telemetry receiver
-tables into a tblRecaptures.
-"""
-# import modules required for function dependencies
-import numpy as np
-import pandas as pd
-import os
-import sqlite3
-import datetime
-import matplotlib.pyplot as plt
-import matplotlib
-import matplotlib.dates as mdates
-from mpl_toolkits.mplot3d import Axes3D
-import statsmodels.api as sm
-import statsmodels.formula.api as smf
-import networkx as nx
-from matplotlib import rcParams
-from scipy import interpolate
-
-font = {'family': 'serif','size': 6}
-rcParams['font.size'] = 6
-rcParams['font.family'] = 'serif'
-
-def the_big_merge(outputWS,projectDB, hitRatio_Filter = False, pre_release_Filter = False, rec_list = None, con_rec_filter = None):
-    '''function takes classified data, merges across sites and then joins presence
-    and overlapping data into one big file for model building.'''
-    conn = sqlite3.connect(projectDB)                                              # connect to the database
-    if rec_list != None:
-        recSQL = "SELECT * FROM tblMasterReceiver WHERE recID = '%s'"%(rec_list[0])
-        for i in rec_list[1:]:
-            recSQL = recSQL + " OR recID = '%s'"%(i)
-    else:
-        recSQL = "SELECT * FROM tblMasterReceiver"                                 # SQL code to import data from this node
-    receivers = pd.read_sql(recSQL,con = conn)                                 # import data
-    receivers = receivers.recID.unique()                                       # get the unique receivers associated with this node
-    recapdata = pd.DataFrame()#columns = ['FreqCode','Epoch','recID','timeStamp','fileName'])                # set up an empty data frame
-    c = conn.cursor()
-
-    bouts = False
-    for i in receivers:                                                            # for every receiver
-
-        print ("Start selecting and merging data for receiver %s"%(i))
-        c.execute("SELECT name FROM sqlite_master WHERE type='table' ORDER BY name;")
-        tbls = c.fetchall()
-        tblList = []
-        for j in tbls:
-            if i in j[0]:
-                tblList.append(j[0])
-            if j[0] == 'tblPresence' or j[0]== 'tblOverlap':
-                bouts = True
-        del j
-        # iterate over the receivers to find the final classification (aka the largest _n)
-        max_iter_dict = {} # receiver:max iter
-        curr_idx = 0
-        max_iter = 1
-        while curr_idx <= len(tblList) - 1:
-            for j in tblList:
-                if int(j[-1]) >= max_iter:
-                    max_iter = int(j[-1])
-                    max_iter_dict[i] = j
-                curr_idx = curr_idx + 1
-        curr_idx = 0
-
-        # once we have a hash table of receiver to max classification, extract the classification dataset
-        for j in max_iter_dict:
-
-            cursor = conn.execute('select * from %s'%(max_iter_dict[j]))
-            names = [description[0] for description in cursor.description]
-
-            if bouts == True:
-                if 'hitRatio_A' in names:
-                    sql = '''SELECT %s.FreqCode, %s.Epoch, %s.recID, timeStamp,presence_number, overlapping, hitRatio_A, hitRatio_M, detHist_A, detHist_M, conRecLength_A, conRecLength_M, lag, lagDiff, test, RelDate
-                    FROM %s
-                    LEFT JOIN tblMasterTag ON %s.FreqCode = tblMasterTag.FreqCode
-                    LEFT JOIN tblOverlap ON %s.FreqCode = tblOverlap.FreqCode AND %s.Epoch = tblOverlap.Epoch AND %s.recID = tblOverlap.recID
-                    LEFT JOIN tblPresence ON %s.FreqCode = tblPresence.FreqCode AND %s.Epoch = tblPresence.Epoch AND %s.recID = tblPresence.recID'''%(max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j])
-                else:
-                    sql = '''SELECT %s.FreqCode, %s.Epoch, %s.recID, timeStamp,presence_number, overlapping,test, RelDate
-                    FROM %s
-                    LEFT JOIN tblMasterTag ON %s.FreqCode = tblMasterTag.FreqCode
-                    LEFT JOIN tblOverlap ON %s.FreqCode = tblOverlap.FreqCode AND %s.Epoch = tblOverlap.Epoch AND %s.recID = tblOverlap.recID
-                    LEFT JOIN tblPresence ON %s.FreqCode = tblPresence.FreqCode AND %s.Epoch = tblPresence.Epoch AND %s.recID = tblPresence.recID'''%(max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j])
-                dat = pd.read_sql(sql, con = conn, coerce_float = True)                     # get data for this receiver
-                dat['overlapping'].fillna(0,inplace = True)
-                #dat = dat[dat.overlapping == 0]
-
-
-            else:
-
-                if 'hitRatio_A' in names:
-                    sql = '''SELECT %s.FreqCode, %s.Epoch, %s.recID, timeStamp, hitRatio_A, hitRatio_M, detHist_A, detHist_M, conRecLength_A, conRecLength_M, lag, lagDiff, test, RelDate
-                    FROM %s
-                    LEFT JOIN tblMasterTag ON %s.FreqCode = tblMasterTag.FreqCode'''%(max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j])
-
-                else:
-                    sql = '''SELECT %s.FreqCode, %s.Epoch, %s.recID, timeStamp, test, RelDate
-                    FROM %s
-                    LEFT JOIN tblMasterTag ON %s.FreqCode = tblMasterTag.FreqCode'''%(max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j],max_iter_dict[j])
-
-                dat = pd.read_sql(sql, con = conn, coerce_float = True)                     # get data for this receiver
-                dat['presence_number'] = np.zeros(len(dat))
-                dat['overlapping'] = np.zeros(len(dat))
-
-            dat = dat[dat.test == 1]
-            dat['RelDate'] = pd.to_datetime(dat.RelDate)
-            dat['timeStamp'] = pd.to_datetime(dat.timeStamp)
-            if hitRatio_Filter == True:
-                dat = dat[(dat.hitRatio_A > 0.10)]# | (dat.hitRatio_M > 0.10)]
-            if con_rec_filter == True:
-                dat = dat[dat.conRecLength_A >= 2]
-            if pre_release_Filter == True:
-                dat = dat[(dat.timeStamp >= dat.RelDate)]
-            recapdata = recapdata.append(dat)
-            del dat
-    c.close()
-
-    recapdata.drop_duplicates(keep = 'first', inplace = True)
-    return recapdata
-
-def vr2_recaps(projectDB, pre_release_Filter = False):
-    '''If the VR2 acoustic study uses large random pulse widths, the false positive
-    reduction algorithm used in BIOTAS is moot.  We will never be able to create
-    a useful detection history, which is central to the algorithm.  However, 
-    we can still use BIOTAS for data management, model building and analysis.
-    
-    This function creates tblRecaptures from tblRaw
-    '''
-    # connect to project database and get tags
-    conn = sqlite3.connect(projectDB)                                              #
-    c = conn.cursor()    
-                                     
-    tags = pd.read_sql("SELECT * FROM tblMasterTag WHERE TagType == 'Study'", con = conn)
-    tags = tags.FreqCode.unique()
-    
-    recapdata = pd.DataFrame()
-    
-    # build a recaptures table
-    for tag in tags:
-        tag_dat = pd.read_sql("SELECT * FROM tblRaw WHERE FreqCode =='%s'"%(tag), con = conn)
-        recapdata = recapdata.append(tag_dat)
-        
-    c.close()
-
-    recapdata.drop_duplicates(keep = 'first', inplace = True)
-    
-    # make all test = 1 and overlapping = 1
-    recapdata['test'] = np.repeat(1,len(recapdata))
-    recapdata['overlapping'] = np.zeros(len(recapdata))
-
-    # return dataframe
-    return recapdata    
-    

pymast-0.0.5.dist-info/METADATA

@@ -1,19 +0,0 @@
-Metadata-Version: 2.1
-Name: pymast
-Version: 0.0.5
-Summary: Movement Analysis Software for Telemetry (MAST) for
-Home-page: https://github.com/knebiolo/mast
-Author: Kevin P. Nebiolo and Theodore Castro-Santos
-Author-email: kevin.nebiolo@kleinschmidtgroup.com
-License: MIT
-Requires-Python: >=3.5
-License-File: LICENSE.txt
-Requires-Dist: numpy >=1.17.4
-Requires-Dist: pandas >=0.25.3
-Requires-Dist: matplotlib >=3.1.1
-Requires-Dist: statsmodels >=0.10.1
-Requires-Dist: networkx >=2.2
-Requires-Dist: scipy >=1.7.1
-Requires-Dist: scikit-learn
-Requires-Dist: h5py
-

pymast-0.0.5.dist-info/RECORD

@@ -1,14 +0,0 @@
-pymast/__init__.py,sha256=lvDHHvhI7UL2F5QLDU_2b62OUnRTlhybslr6aTn27Z0,538
-pymast/fish_history.py,sha256=XaubGDRLfR89v2rIrFvkf7AKOLMTA5z--KyCJoXqnv4,6822
-pymast/formatter.py,sha256=Iq0VYtA-U7j7z7e-5H1OfRd0uP5dod2ptOKs2GK8hlc,58555
-pymast/naive_bayes.py,sha256=pjB8LSIFM8-fW7sohy5gCuFgKk1VP5yh63raMp9mdEU,6475
-pymast/overlap_removal.py,sha256=4SwP8qZDqEYZ6_I0xGlI6647bTt45EaGDP5FxbqddZo,25416
-pymast/parsers.py,sha256=b5H_a6tv0RxlNe_NhdnjJilA30Uo9kDq8w8WGP6bT8s,59248
-pymast/predictors.py,sha256=VEWnhxgJcbnag8h6DNpWbeWgGiK9YyV_3N4xkcJFjdo,8018
-pymast/radio_project.py,sha256=QT9l_qyZTKWqTu55kpgIESPDR1dnjajEQlUBYSg0H8Q,55502
-pymast/table_merge.py,sha256=7_z4F_q3DW3RFXruRH6Qanum7E5QQQnu_w6qyyW-YVc,7921
-pymast-0.0.5.dist-info/LICENSE.txt,sha256=CX_nvzXXwOA7SPq4-ivN4Q9NIK2PfK-KGHt3ZQKldsw,1143
-pymast-0.0.5.dist-info/METADATA,sha256=JQhu_VTKXY3Hxr6-boeylXBqVR3ywx4iiwu0dymRM1M,577
-pymast-0.0.5.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-pymast-0.0.5.dist-info/top_level.txt,sha256=LDZpLLge9zI4yvuMYoABLrsOrZzE3bYDRULmHoZQc4k,7
-pymast-0.0.5.dist-info/RECORD,,