ProtParser.py.old

#!/usr/bin/python

import os
import sys
import glob
import time
# import elementtree
import xml.etree.ElementTree as ET  # imports element tree function

# tree = ET.parse('HYPER ACUTE STROKE.xml')  #uses ET function on the xml file

# path = 'c/Users/msveiven/Desktop/Professor_Saranathan_Research/WIKIPROTPATHTEST'
# print('Path is ' + path)
# f = os.path.getmtime('webpageCreator.py')


# path = os.environ['WIKIPROTPATH']+'websiteCreator.py'
# print('this is the ' + path)
# f = os.path.getmtime(path)


if len(sys.argv) != 2:
    print('The correct number of arguments is 1. Write this: "python $WIKIPROTPATH/ProtParser.py <xml_file_name>. Run space_to_underscore.py if your xml files have spaces in their names.')
    print('If you want to do all of the xml files in a directory. Go to that directory and write this: "python $WIKIPROTPATH/ProtParser.py all".')
    print(' If you want to run protparser on all the xml files in the branches of Scanners, write this:  "python $WIKIPROTPATH/ProtParser.py all_directories".')
    sys.exit()

else:
    xmlfile = sys.argv[1]



def ProtParser(series):
    if os.path.exists(series) != True:
        #print(os.path.exists(series))
        print(series+'\n')
        print(series+' does not exist in current working directory')
        sys.exit()
    tree = ET.parse(series)  # uses ET function on the xml file
    root = tree.getroot()  # creates root function for calling roots from the xml file. root[0] calls the first child in the element tree
    print('Now parsing '+series+'!')
    tocExists = 0
    currentPath = os.getcwd()
    #    print(currentPath.split("Scanners")[0]+'customParameters')
    #    print(currentPath.split("Scanners")[0]+'complexParameters')

    if root[0].tag == 'PrintTOC':
        tocExists = 1
    if os.path.isfile('customParameters.txt') == True and os.path.isfile('complexParameters.txt') == True:
        parameterList = [line.rstrip('\n') for line in
                         open('customParameters.txt')]  # creates a list by reading parameters from text file

        complexParameterList = [line.rstrip('\n') for line in open('complexParameters.txt')]
    elif os.path.isfile(os.environ['WIKIPROTPATH'] + 'customParameters.txt') == True and os.path.isfile(
                    os.environ['WIKIPROTPATH'] + 'complexParameters.txt') == True:
        parameterList = [line.rstrip('\n') for line in open(os.environ[
                                                                'WIKIPROTPATH'] + 'customParameters.txt')]  # creates a list by reading parameters from text file
        complexParameterList = [line.rstrip('\n') for line in
                                open(os.environ['WIKIPROTPATH'] + 'complexParameters.txt')]
    else:
        print('No text files found!')
        sys.exit()

    scanTimeSearched = 0

    protocolCount = 0
    loopCounter = 0
    scanLooper = 0

    parameterListSize = len(parameterList)  # size up the number of parameters
    complexParameterListSize = len(complexParameterList)

    while loopCounter < 100:  # this while loop finds the number of protocols
        try:
            print(root[loopCounter].text)
            loopCounter += 1
        except Exception:
            protocolCount = loopCounter - tocExists
            loopCounter = 100
            pass

    parameterListSize += 1  # adds 1 to size of parametersList so we have extra column
    complexParameterListSize += 1

    Matrix1 = [['-' for x in range(parameterListSize)] for y in
               range(protocolCount + 1)]  # creates a 2D array with size parameter list by protocol number
    Matrix2 = [['-' for x in range(protocolCount + 1)] for y in range(complexParameterListSize + 1)]
    Matrix1[0][0] = 'Series'
    Matrix2[0][0] = 'Sequence Paramters'

    Matrix3 = [['-' for x in range(2)] for y in range(protocolCount + 1)]

    parameterLooper = 0

    while parameterLooper < parameterListSize - 1:  # populates first row with parameters

        Matrix1[0][parameterLooper + 1] = parameterList[parameterLooper].split('->')[1]
        parameterLooper += 1

    parameterLooper = 0

    while parameterLooper < complexParameterListSize - 1:  # populates first row with parameters

        Matrix2[parameterLooper + 1][0] = complexParameterList[parameterLooper].split('->')[
            1]  # First column for localizer
        parameterLooper += 1

    try:
        localizerLooper = 0

        while localizerLooper < protocolCount:  # populates first row with parameters

            Matrix2[0][localizerLooper + 1] = root[localizerLooper][0][1][0][0].text[50:]
            localizerLooper += 1

    except Exception:
        localizerLooper = 1
        while localizerLooper < protocolCount + 1:  # populates first row with parameters

            Matrix2[0][localizerLooper] = root[0][0][2][0][0][0][localizerLooper - 1].get('name')
            localizerLooper += 1

    try:
        scanLooper = 0
        while scanLooper < protocolCount:  # this while loop populates the name of scans in the first column
            Matrix1[scanLooper + 1][0] = root[scanLooper][0][1][0][0].text[50:]
            scanLooper += 1
    except Exception:
        scanLooper = 0
        while scanLooper < protocolCount:  # this while loop populates the name of scans in the first column
            Matrix1[scanLooper + 1][0] = root[0][0][2][0][0][0][scanLooper].get('name')
            scanLooper += 1

    def findSearchItem(Matrix, searchitem, num, searchItemFound):  # define function that searches for each term
        j = 0
        totalScanTime = '0:0'
        while j < 100:
            k = 0
            if searchitem.split('->')[0] == 'Scan time' and (j < protocolCount + 1):
                try:
                    if Matrix == 1:
                        Matrix1[j + 1 - tocExists][num + 1] = root[j][0][1][0][1].text[3:9]
                        totalScanTime = str(
                            int(totalScanTime.split(':')[0]) + int(root[j][0][1][0][1].text[3:9].split(':')[0]) + (
                                int(totalScanTime.split(':')[1]) + int(
                                    root[j][0][1][0][1].text[3:9].split(':')[1])) // int(
                                60)) + ':' + str((
                                                     int(totalScanTime.split(':')[1]) + int(
                                                         root[j][0][1][0][1].text[3:9].split(':')[1])) % 60)
                    if Matrix == 2:
                        Matrix2[num + 1][j + 1 - tocExists] = root[j][0][1][0][1].text[3:9]
                        totalScanTime = str(
                            int(totalScanTime.split(':')[0]) + int(root[j][0][1][0][1].text[3:9].split(':')[0]) + (
                                int(totalScanTime.split(':')[1]) + int(
                                    root[j][0][1][0][1].text[3:9].split(':')[1])) // int(
                                60)) + ':' + str((
                                                     int(totalScanTime.split(':')[1]) + int(
                                                         root[j][0][1][0][1].text[3:9].split(':')[1])) % 60)
                except Exception:
                    pass

            while k < 100:
                l = 0
                while l < 100:
                    try:
                        if root[j][0][1][k][l][0].text == searchitem.split('->')[
                            0]:  # check to see if search item has been found
                            if Matrix == 1:
                                Matrix1[j + 1 - tocExists][num + 1] = root[j][0][1][k][l][
                                    1].text  # places the parameter value in the Matrix1
                            if Matrix == 2:
                                Matrix2[num + 1][j + 1 - tocExists] = root[j][0][1][k][l][1].text
                            searchItemFound = 1  # variable that shows that a search item has been found
                            k = 100  # sets k and l to 100 to break out of the two while loops so that we can move to the next
                            l = 100  # protocol, which prevents redundancies

                            if Matrix == 1:
                                Matrix1[j][num + 1] = root[j][0][1][k][l][
                                    1].text  # adding value of parameter to Matrix1
                            if Matrix == 2:
                                Matrix2[num + 1][j] = root[j][0][1][k][l][1].text

                        if searchitem.split('->')[0] == 'PAT':
                            if Matrix == 1:
                                Matrix1[j + 1 - tocExists][num + 1] = root[j][0][1][0][1].text.split()[8]
                            if Matrix == 2:
                                Matrix2[num + 1][j + 1 - tocExists] = root[j][0][1][0][1].text.split()[8]

                    except Exception:  # prevents error from stopping script when element does not exist
                        pass
                    l += 1
                k += 1
            j += 1
        return (searchItemFound, totalScanTime)

    parameterCounter = 0
    scanTimeSum = '0:0'

    for parameter in parameterList:  # for loop to search for each parameter key word in parameterlist
        searchItemExists = 0
        if parameter.split('->')[0] == 'Scan time':
            scanTimeSum = findSearchItem(1, parameter, parameterCounter, searchItemExists)[1]
        elif parameter.split('->')[0] == 'PAT':
            findSearchItem(1, parameter, parameterCounter, searchItemExists)
        elif parameter.split('->')[0] == 'Matrix':
            matrix1Looper = 1

            while matrix1Looper < protocolCount + 1:  # multiplies the values of the phase and base resolution and inputs to the Matrix1
                try:
                    Matrix1[matrix1Looper][8] = str(Matrix1[matrix1Looper][6]) + 'X ' + str(
                        int(Matrix1[matrix1Looper][6]) * int(Matrix1[matrix1Looper][7].split("%")[0]) / 100)
                except Exception:
                    Matrix1[matrix1Looper][6] or [matrix1Looper][7].split("%")[0] == '-'
                    pass
                matrix1Looper += 1

            searchItemExists = 1

        elif parameter == 'Notes':
            searchItemExists = 1
        elif findSearchItem(1, parameter, parameterCounter, searchItemExists)[0] == 0 and parameter.split('->')[
            0] != 'Notes':  # calls search function to find each search parameter in parameterList
            print("Warning! Parameter %s not found! Check spelling and full parameter name \n" %
                  parameter.split('->')[0])  # prints a warning if the parameter called does not exist
        parameterCounter += 1

    parameterCounter = 0
    for complexParameter in complexParameterList:  # for loop to search for each parameter key word in parameterlist
        searchItemExists = 0
        if complexParameter.split('->')[0] == 'Scan time':
            scanTimeSum = findSearchItem(2, complexParameter, parameterCounter, searchItemExists)[1]
        elif complexParameter.split('->')[0] == 'PAT':
            findSearchItem(2, complexParameter, parameterCounter, searchItemExists)
        elif complexParameter.split('->')[0] == 'Matrix':
            matrix2Looper = 1

            while matrix2Looper < protocolCount + 1:  # multiplies the values of the phase and base resolution and inputs to the Matrix2

                try:
                    Matrix2[10][matrix2Looper] = str(Matrix2[8][matrix2Looper]) + 'X ' + str(
                        int(Matrix2[8][matrix2Looper]) * int(Matrix2[9][matrix2Looper].split("%")[0]) / 100)
                except Exception:
                    Matrix2[8][matrix2Looper] or Matrix2[9][matrix2Looper] == '-'
                    pass
                matrix2Looper += 1
            searchItemExists = 1
        elif complexParameter == 'Notes':
            searchItemExists = 1
        elif findSearchItem(2, complexParameter, parameterCounter, searchItemExists)[0] == 0 and \
                        complexParameter.split('->')[
                            0] != 'Notes':  # calls search function to find each search parameter in parameterList
            print("Warning! Parameter %s not found! Check spelling and full parameter name \n" %
                  complexParameter.split('->')[0])  # prints a warning if the parameter called does not exist
        parameterCounter += 1

    printLooper1 = 0

#    while printLooper1 < protocolCount + 1:  # prints the Matrix1 one row at a time
#        print(Matrix1[printLooper1])
#        printLooper1 += 1

    printLooper2 = 0

   # while printLooper2 < complexParameterListSize:  # prints the Matrix2 one row at a time
        #print(Matrix2[printLooper2])
  #      printLooper2 += 1

    Matrix1[0][parameterListSize - 1] = '____________Notes____________'
    seriesName = root[0][0][2][0][0][0].get('name')
    seriesNameFile = seriesName.replace(" ", "_")
    seriesNameFile = seriesName.replace("/", "_") + '.htm'

    # f1 = open('masterList.htm', 'r')

    # f1.write('<!DOCTYPE html> \n')
    # f1.write('<html>\n')
    # f1.write('<body>\n')
    # f1.write('<A HREF = "file:///C:/Users/msveiven/PycharmProjects/untitled/scriptOutput1.htm">B5 - BRN MS</A>\n')
    # f1.write('</body>\n')
    # f1.write('</html>\n')

    # f1.seek(0)
    # s = f1.read()
    # R = s.split('</body>')

    # f1.close()

    # f1 = open('masterList.htm', 'w')
    # f1.write(R[0])
    # f1.write('<p>\n')
    # f1.write('<A HREF = "file:///C:/Users/kevcron35/PycharmProjects/untitled/')
    # f1.write(seriesNameFile)
    # f1.write('">')
    # f1.write(seriesName+' Updated '+time.strftime("%d.%m.%Y"))
    # f1.write('</A>\n')
    # f1.write('</p>\n')
    # f1.write('</body>\n')
    # f1.write('</html>\n')

    # f1.close()
    currentPath = os.getcwd()
    seriesNameFile = currentPath + "/" + seriesNameFile
    f = open(seriesNameFile, 'w+')  # REST OF SCRIPT IS WRITING HTML FILE

    f.write('<!DOCTYPE html> \n')
    f.write('<html>\n')
    f.write('<head>\n')
    f.write('<style>\n')
    f.write('table, th, td {\n')
    f.write('\t border: 1px solid black;\n')
    f.write('}\n')
    f.write('th, td { \n \t padding: 15px;\n}')
    f.write('</style>\n')
    f.write('</head>\n')
    f.write('<body>\n')

    if tocExists == 1:

        f.write('<h1>')
        f.write(root[0][0][2][0][0][0].get('name'))

        f.write(' (Total scan time: ' + scanTimeSum.split(':')[0] + ':' + scanTimeSum.split(':')[1] + ')')
        f.write('</h1>\n')
        f.write('<h2>')
        f.write('Overview')
        f.write('</h2>\n')

    else:
        f.write('<h1>')
        f.write(root[0][0][1][0][0].text[35:49])
        f.write(' (Total scan time: ' + scanTimeSum.split(':')[0] + ':' + scanTimeSum.split(':')[1] + ' min)')
        f.write('</h1>\n')

    f.write('<table style="width:100%">\n')

    writeCounterColumn1 = 0

    while writeCounterColumn1 < 1:

        writeCounterRow1 = 0

        f.write('<table style="background-color:#FFFFE0;"> \n')
        f.write('<tr style="background-color:#BDB76B;color:ffffff;"> \n')
        while writeCounterRow1 < parameterListSize:
            f.write('<th>')
            f.write(str(Matrix1[writeCounterColumn1][writeCounterRow1]))
            f.write('</th>')
            writeCounterRow1 += 1
        f.write('</tr>')
        f.write('\n')
        writeCounterColumn1 += 1

    writeCounterColumn1 = 1

    while writeCounterColumn1 < protocolCount + 1:

        writeCounterRow1 = 0
        f.write('<tr>')
        while writeCounterRow1 < parameterListSize:
            f.write('<td>')
            f.write(Matrix1[writeCounterColumn1][writeCounterRow1])
            f.write('</td>')
            writeCounterRow1 += 1
        f.write('</tr>')
        f.write('\n')
        writeCounterColumn1 += 1

    f.write('</table>\n')
    f.write('<br>')
    f.write('</br>')
    f.write('\n')
    f.write('<table style="width:100%">\n')

    writeCounterColumn2 = 0

    while writeCounterColumn2 < 1:

        writeCounterRow2 = 0

        f.write('<table style="background-color:#CAE8FC;"> \n')
        f.write('<tr style="background-color:#0613D7;color:#FBFBFC;"> \n')
        while writeCounterRow2 < protocolCount + 1:
            f.write('<th>')
            f.write(Matrix2[writeCounterColumn2][writeCounterRow2])
            f.write('</th>')
            writeCounterRow2 += 1
        f.write('</tr>')
        f.write('\n')
        writeCounterColumn2 += 1

    f.write('<h2>\n')
    f.write('Detailed')
    f.write('\n')
    f.write('</h2>\n')

    writeCounterColumn2 = 1

    while writeCounterColumn2 < complexParameterListSize:

        writeCounterRow2 = 0
        f.write('<tr>')
        while writeCounterRow2 < protocolCount + 1:
            f.write('<td>')
            f.write(Matrix2[writeCounterColumn2][writeCounterRow2])
            f.write('</td>')
            writeCounterRow2 += 1
        f.write('</tr>')
        f.write('\n')
        writeCounterColumn2 += 1

    f.write('</table>\n')
    f.write('\n')
    f.write('<br>')
    f.write('</br>')
    f.write('<textarea rows="6" cols="140">')
    f.write('Insert notes here')
    f.write('</textarea>')
    f.write('<br>')
    f.write('</br>')
    f.write('<textarea rows="6" cols="140">')
    f.write('Indications')
    f.write('</textarea>')
    f.write('<br>')
    f.write('</br>')
    f.write('<img src=')
    f.write('"')
    f.write(series.split('xml')[0])
    f.write('jpg')
    f.write('"')
    f.write(' alt="Placer Image" style="width:304px;height:228px;">')
    f.write('</body>\n')
    f.write('<html>\n')
    f.close()
    return

def protParserAll():
    import space_to_underscore
    space_to_underscore.spaceToUnderscore()

    currentPath = os.getcwd()
    path = currentPath + "/*.xml"

    for gname in glob.glob(path):
        path = currentPath + "/*.xml"
#        print(path)
        g = os.path.getmtime(gname)
        htmlFile = gname.split(".")[0] + ".htm"
#        print(htmlFile)
        path = currentPath + "/"
#        print(path)
        if os.path.exists(htmlFile):
            f = os.path.getmtime(htmlFile)

            if f < g:
                ProtParser(gname)

            else:
                print('ProtParser has already run on ' + gname+'\n')

        else:
            ProtParser(gname)
    return

if xmlfile.endswith('all') or xmlfile.endswith('ALL'):
    print('All xml files in current directory will be run through protParser now!')
    protParserAll()

elif xmlfile.endswith('all_directories') or xmlfile.endswith('ALL_DIRECTORIES'):
    print('Will now run ProtParser on all xml files in directories in form like this: "$WIKIPROTPATH/Scanners/SCANNER_NAME/NEURO"')
    owd = os.environ['WIKIPROTPATH'] + 'Scanners/'
    os.chdir(owd)
    #print(os.getcwd())
    directoryList1 = next(os.walk('.'))[1]
    #print(directoryList1)


    i = 0
    while (i < len(directoryList1)):
        if (directoryList1[i] != 'apps'):
            if (directoryList1[i] != 'files'):
                if (directoryList1[i] != 'uploads'):
                    if (directoryList1[i] != '.idea'):

                        os.chdir(directoryList1[i])
                        #print(directoryList1[i])
                        directoryList2 = next(os.walk('.'))[1]
                        sowd = os.getcwd()


                        j = 0
                        while (j < len(directoryList2)):
                            if (directoryList2[j] != 'apps'):
                                if (directoryList2[j] != 'files'):
                                    if (directoryList2[j] != 'uploads'):
                                        if (directoryList2[j] != '.idea'):
                                            #print('Inside second loop')
                                            branch_directory = directoryList2[j]
                                            os.chdir(branch_directory)
                                            #print(branch_directory)
                                            #print(os.path.abspath(directoryList2[j]))
                                           # print(os.getcwd())

                                            protParserAll()
                                            os.chdir(sowd)
                            j = j + 1
                        os.chdir(owd)
        i = i + 1


else:
    if xmlfile.endswith('.xml'):
        ProtParser(sys.argv[1])
    else:
        print('File name must end in .xml. ')
        print('If you would like all .xml files parsed in all directories type "python $WIKIPROTPATH/ProtParser.py all_directories".')
        print('If you would like all the .xml files parsed in a single directory. Go to that directory and type "python $WIKIPROTPATH/ProtParser.py all".')