Source code for MapParser

## TEMPY is a Python library designed to help the user manipulate and analyse atomic structures and density maps from 3D EM. 
## Copyright (c) 2013 Daven Vasishtan,Irene Farabella, Arun Prasad Pandurangan, Harpal Sahota, Frank Alber and Maya Topf



#--Global imports--#
import numpy
from numpy import array, fromfile, flipud
import struct as binary
import string

#--Local imports--#
from EMMap import * 

class MapParser:
    """
    A class to read various EM map file types into a Map object instance.
    """

    def __init__(self):
        ## mapping of numpy type to MRC mode
        self.numpy2mrc = {
            ## convert these to int8
            numpy.uint8: 0,
            numpy.bool: 0,
            numpy.bool_: 0,

            ## convert these to int16
            numpy.int16: 1,
            numpy.int8: 1,

            ## convert these to float32
            numpy.float32: 2,
            numpy.float64: 2,
            numpy.int32: 2,
            numpy.int: 2,

            ## convert these to complex64
            numpy.complex: 4,
            numpy.complex64: 4,
            numpy.complex128: 4,

            ## convert these to uint16
            numpy.uint16: 6,
        }

    @staticmethod
    def readMRCHeader(filename, endian = '<'):
        f = open(filename,'rb')
        fm_string = endian+(10*'l')+(6*'f')+(3*'l')+(3*'f')+(27*'l')+(3*'f')+(4*'c')+'lfl'
        header = list(binary.unpack(fm_string, f.read(224)))
        notes = f.read(800)
        notes = string.replace(notes, '\x00', '')
        header.append(notes)
        header = tuple(header)
        f.close()
        return header

    @staticmethod
    def get_endian(filename):
        h = MapParser.readMRCHeader(filename)
        if 0 <= h[3] <= 6:
            endian = '<'
        else:
            endian = '>'
        return endian

    @staticmethod
    def readMRC(filename):
        
        mrc2numpy = {
            0: numpy.uint8,
            1: numpy.int16,
            2: numpy.float32,
            #	3:  complex made of two int16.  No such thing in numpy
            #   however, we could manually build a complex array by reading two
            #   int16 arrays somehow.
            4: numpy.complex64,
            6: numpy.uint16,    # according to UCSF
        }

        endian = MapParser.get_endian(filename)
        header = MapParser.readMRCHeader(filename, endian)

        box_size = tuple(flipud(header[0:3]))
        origin = header[49:52] #ctrl UCSF
        apix = header[10]/header[0]
        map_size = header[0]*header[1]*header[2]

        f = open(filename,'rb')
        f.seek(1024)
        map_data = fromfile(f, dtype=mrc2numpy[header[3]], count=map_size)
        map_data=map_data.reshape(box_size)
        map_data=array(map_data, dtype='float64')
        f.close()
        return Map(map_data, origin, apix, filename, header=header)

    #BROKEN
    @staticmethod
    def readXPLOR(filename, user_origin=None, user_box_size=None):
        f = open(filename, 'r')
        while(True):
            l = f.readline().split()
            #print l
            if(len(l) ==1 and l[0] == '0'):
                break
        new_map = []
        line = 1
        while(True):
            line = f.readline().split()
            for dens in line:
                new_map.append(float(dens))
            if len(new_map) >= box_size[0]*box_size[1]*box_size[2]:
                break
        new_map = array(new_map)
        new_map = new_map.reshape(box_size[2], box_size[1], box_size[0])
        f.close()
        return Map(new_map, origin, box_size, apix)

    @staticmethod
    def readSitus(filename):
        f = open(self.filename, 'r')
        first_line = f.readline().split()
        apix = float(first_line[0])
        origin = map(float, first_line[1:4])
        box_size = map(int, first_line[4:7])
        new_map = []
        line = 1
        while(True):
            line = f.readline().split()
            for dens in line:
                new_map.append(float(dens))
            if len(new_map) >= box_size[0]*box_size[1]*box_size[2]:
                break
        new_map = array(new_map)
        new_map = new_map.reshape(box_size[2], box_size[1], box_size[0])
        f.close()
        return Map(new_map, origin, box_size, apix)