#  This file is part of AISelect.

#  AISelect is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.

#  AISelect is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with AISelect.  If not, see <http://www.gnu.org/licenses/>.


import math, bioformats
import numpy as np
import javabridge
from bs4 import BeautifulSoup
import logging

from settings import Global


class BioMeta(object):
    def __init__(self, filepath, standalone=True, series=0):

        self.filepath = filepath
        self.date = 0
        self.sizex = 0
        self.sizey = 0
        self.sizez = 0
        self.frames = 0
        self.sizet = 0
        self.sizec = 3
        self.series = 0

        # self.physicalsizet = float(image.find("Pixels").attrs[""])
        self.physicalsizex = 1
        self.physicalsizey = 1
        self.physicalsizexunit = "mm"
        self.physicalsizeyunit = "mm"

        if standalone: javabridge.start_vm(class_path=bioformats.JARS)

        try:
            self.metadata_unparsed = bioformats.get_omexml_metadata(filepath)
            self.metadata = BeautifulSoup(self.metadata_unparsed, "xml")
            # defaultseries
            self.setSeries(series)
            self.query_metadata()
        except:
            raise Exception("BioMeta needs to be run in standalone Mode to initialize Javabridge")
        finally:
            logging.info("BioMeta parsed")

    def getSeriesCount(self):
        return self.seriesamount

    def setSeries(self, it):
        self.series = it
        return self

    def intializeFromTiff(self):

        self.date = "1.3.91"


    def run(self):
        image = self.allmetadata[self.series]
        try:
            print(int(image.find("Pixels").attrs["SizeT"]))
            self.date = str(image.find("AcquisitionDate").contents[0]) if image.find("AcquisitionDate") is not None else "NOT-SET"
            self.sizex = int(image.find("Pixels").attrs["SizeX"]) if image.find("Pixels").attrs["SizeX"] is not None else 0
            self.sizey = int(image.find("Pixels").attrs["SizeY"]) if image.find("Pixels").attrs["SizeY"] is not None else 0
            self.sizez = int(image.find("Pixels").attrs["SizeZ"]) if image.find("Pixels").attrs["SizeZ"] is not None else 0
            self.frames = int(image.find("Pixels").attrs["SizeT"]) if image.find("Pixels").attrs["SizeT"] is not None else 0
            self.sizet = int(image.find("Pixels").attrs["SizeT"]) if image.find("Pixels").attrs["SizeT"] is not None else 0
            self.sizec = int(image.find("Pixels").attrs["SizeC"]) if image.find("Pixels").attrs["SizeC"] is not None else 0

            # self.physicalsizet = float(image.find("Pixels").attrs[""])
            self.physicalsizex = float(image.find("Pixels").attrs["PhysicalSizeX"]) if image.find("Pixels").attrs["PhysicalSizeX"] is not None else 1
            self.physicalsizey = float(image.find("Pixels").attrs["PhysicalSizeY"]) if image.find("Pixels").attrs["PhysicalSizeY"] is not None else 1
            self.physicalsizexunit = image.find("Pixels").attrs["PhysicalSizeXUnit"] if image.find("Pixels").attrs["PhysicalSizeXUnit"] is not None else "Pixels"
            self.physicalsizeyunit = image.find("Pixels").attrs["PhysicalSizeYUnit"] if image.find("Pixels").attrs["PhysicalSizeYUnit"] is not None else "Pixels"
        except:
            print("ITS NOT A VALID BIOIMAGEFILE")
        finally:
            return self

    def query_metadata(self):
        self.allmetadata = self.metadata.findAll("Image")
        self.seriesamount = len(self.allmetadata)

    def getChannelNames(self):

        channelexplain = Global.colorReadableMap
        try:
            channellist = [i.attrs["Name"]+" (" + channelexplain[index]+ ")" for index,i in enumerate(self.allmetadata[self.series].findAll("Channel"))]
            return channellist
        except:
            channellist = [channelexplain[i] for i in range(self.sizec)]
            return channellist

    def getSeriesName(self):
        try:
            seriesname = self.allmetadata[self.series].attrs["Name"]
        except:
            seriesname = "Not Specified"
        return seriesname

    def getDirName(self):
        return "AIS" + self.getFileName()

    def getFileName(self):
        return self.filepath.split("/")[-1].split(".")[0]

    def __str__(self):
        return str(self.allmetadata[self.series])


class BioImageFile(object):
    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        # Initialize JAVABRIDGE
        javabridge.start_vm(class_path=bioformats.JARS)

        self.meta = BioMeta(filepath=filepath, standalone=False)

        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c

        # STANDARD SETTINGS HERE
        self.debug = debug
        self.series = 0
        self.setz = 0

        #META
        self.shape = (0,0,0) #TODO: setRoutines
        self.bioshape = (0,0,0)

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True

        # Must be run before Picture is correctly processed
        self.readMeta()
        self.readFile()

        return self

    def getImage(self, z=0, t=0):
        assert (self.ran is True), "BioimageFile has no been instatiated"
        #TODO: THIs is to dirty and needs invastigating
        image = self.file[:, :, :, z, t]
        import scipy.misc
        cvimg = scipy.misc.toimage(image)
        img = np.array(cvimg)
        return img

    def getChannel(self, c=0, z=0, t=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        return self.file[:, :, c, z, t]

    def getVideo(self, z=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self,start,end, t=0):
        print("Slized Stack",start,end)
        file = self.getFile()
        return file[:,:,:,start:end,t]


    def readFile(self):

        assert (self.ran is True), "BioimageFile has no been instatiated"

        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.sizec, self.meta.sizez, self.meta.sizet))
        print("Channels:", self.meta.sizec)
        print("T-Size:",self.meta.sizet)
        print("Z-Size:",self.meta.sizez)
        # Debug settings
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):

                        # bioformats appears to swap axes for tif images and read all three channels at a time for RGB
                        im1 = reader.read(c=c, z=z, t=t, series=self.series, rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if (im1.shape[2] == 3):
                                # Three channels are red
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if (self.meta.sizex == im2.shape[1]) and (self.meta.sizey == im2.shape[0]) and not self.meta.sizex == self.meta.sizey:
                            # x and y are swapped
                            #logging.warning("Image might be transposed. Not Swapping")
                            #im3 = im2.transpose()
                            im3 = im2.transpose()
                        else:
                            im3 = im2


                        self.file[:, :, c, z, t] = im3



        #needs to check if image is in rgb format to display


    def colorMap(self,map):

        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3, self.file.shape[3], self.file.shape[4]))

        if len(map) != self.file.shape[2]:
            print("Less then 3 Channels, try different mapping")
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3, self.file.shape[3], self.file.shape[4]))

        for index, mappedchannel in enumerate(map):
            print( "To", index, "Mapped", mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0], self.file.shape[1], self.file.shape[3], self.file.shape[4]))
            else:
                emptyfile[:,:,index,:,:] = self.file[:,:,mappedchannel,:,:]

        print("Returned colormap shape", emptyfile.shape)
        return emptyfile

    def checkDimensions(self,file):
        # unnecessary step

        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape[3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile


        assert self.file.shape[2] == 3, "File Dimensions are wrong"

        return self.file


    def getFile(self):

        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
       # self.checkedfile = self.checkDimensions(self.mappedfile)

        return self.mappedfile


    def getMeta(self):

        return self.meta

    def readMeta(self):
        self.meta.run()
        pass
649835bef078199f468bd16e75c62b035fc3beb6
<mask token>


class BioImageFile(object):

    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        javabridge.start_vm(class_path=bioformats.JARS)
        self.meta = BioMeta(filepath=filepath, standalone=False)
        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c
        self.debug = debug
        self.series = 0
        self.setz = 0
        self.shape = 0, 0, 0
        self.bioshape = 0, 0, 0

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True
        self.readMeta()
        self.readFile()
        return self
    <mask token>
    <mask token>

    def getVideo(self, z=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self, start, end, t=0):
        print('Slized Stack', start, end)
        file = self.getFile()
        return file[:, :, :, start:end, t]

    def readFile(self):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.
            sizec, self.meta.sizez, self.meta.sizet))
        print('Channels:', self.meta.sizec)
        print('T-Size:', self.meta.sizet)
        print('Z-Size:', self.meta.sizez)
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True
            ) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):
                        im1 = reader.read(c=c, z=z, t=t, series=self.series,
                            rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if im1.shape[2] == 3:
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if self.meta.sizex == im2.shape[1
                            ] and self.meta.sizey == im2.shape[0
                            ] and not self.meta.sizex == self.meta.sizey:
                            im3 = im2.transpose()
                        else:
                            im3 = im2
                        self.file[:, :, c, z, t] = im3

    def colorMap(self, map):
        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
            self.file.shape[3], self.file.shape[4]))
        if len(map) != self.file.shape[2]:
            print('Less then 3 Channels, try different mapping')
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
                self.file.shape[3], self.file.shape[4]))
        for index, mappedchannel in enumerate(map):
            print('To', index, 'Mapped', mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0],
                    self.file.shape[1], self.file.shape[3], self.file.shape[4])
                    )
            else:
                emptyfile[:, :, index, :, :] = self.file[:, :,
                    mappedchannel, :, :]
        print('Returned colormap shape', emptyfile.shape)
        return emptyfile

    def checkDimensions(self, file):
        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape
                [3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile
        assert self.file.shape[2] == 3, 'File Dimensions are wrong'
        return self.file

    def getFile(self):
        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
        return self.mappedfile

    def getMeta(self):
        return self.meta

    def readMeta(self):
        self.meta.run()
        pass

<mask token>


class BioMeta(object):
    <mask token>
    <mask token>
    <mask token>
    <mask token>

    def run(self):
        image = self.allmetadata[self.series]
        try:
            print(int(image.find('Pixels').attrs['SizeT']))
            self.date = str(image.find('AcquisitionDate').contents[0]
                ) if image.find('AcquisitionDate') is not None else 'NOT-SET'
            self.sizex = int(image.find('Pixels').attrs['SizeX']
                ) if image.find('Pixels').attrs['SizeX'] is not None else 0
            self.sizey = int(image.find('Pixels').attrs['SizeY']
                ) if image.find('Pixels').attrs['SizeY'] is not None else 0
            self.sizez = int(image.find('Pixels').attrs['SizeZ']
                ) if image.find('Pixels').attrs['SizeZ'] is not None else 0
            self.frames = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizet = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizec = int(image.find('Pixels').attrs['SizeC']
                ) if image.find('Pixels').attrs['SizeC'] is not None else 0
            self.physicalsizex = float(image.find('Pixels').attrs[
                'PhysicalSizeX']) if image.find('Pixels').attrs['PhysicalSizeX'
                ] is not None else 1
            self.physicalsizey = float(image.find('Pixels').attrs[
                'PhysicalSizeY']) if image.find('Pixels').attrs['PhysicalSizeY'
                ] is not None else 1
            self.physicalsizexunit = image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] is not None else 'Pixels'
            self.physicalsizeyunit = image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] is not None else 'Pixels'
        except:
            print('ITS NOT A VALID BIOIMAGEFILE')
        finally:
            return self
    <mask token>
    <mask token>
    <mask token>

    def getDirName(self):
        return 'AIS' + self.getFileName()

    def getFileName(self):
        return self.filepath.split('/')[-1].split('.')[0]
    <mask token>


class BioImageFile(object):

    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        javabridge.start_vm(class_path=bioformats.JARS)
        self.meta = BioMeta(filepath=filepath, standalone=False)
        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c
        self.debug = debug
        self.series = 0
        self.setz = 0
        self.shape = 0, 0, 0
        self.bioshape = 0, 0, 0

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True
        self.readMeta()
        self.readFile()
        return self

    def getImage(self, z=0, t=0):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        image = self.file[:, :, :, z, t]
        import scipy.misc
        cvimg = scipy.misc.toimage(image)
        img = np.array(cvimg)
        return img

    def getChannel(self, c=0, z=0, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, c, z, t]

    def getVideo(self, z=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self, start, end, t=0):
        print('Slized Stack', start, end)
        file = self.getFile()
        return file[:, :, :, start:end, t]

    def readFile(self):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.
            sizec, self.meta.sizez, self.meta.sizet))
        print('Channels:', self.meta.sizec)
        print('T-Size:', self.meta.sizet)
        print('Z-Size:', self.meta.sizez)
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True
            ) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):
                        im1 = reader.read(c=c, z=z, t=t, series=self.series,
                            rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if im1.shape[2] == 3:
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if self.meta.sizex == im2.shape[1
                            ] and self.meta.sizey == im2.shape[0
                            ] and not self.meta.sizex == self.meta.sizey:
                            im3 = im2.transpose()
                        else:
                            im3 = im2
                        self.file[:, :, c, z, t] = im3

    def colorMap(self, map):
        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
            self.file.shape[3], self.file.shape[4]))
        if len(map) != self.file.shape[2]:
            print('Less then 3 Channels, try different mapping')
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
                self.file.shape[3], self.file.shape[4]))
        for index, mappedchannel in enumerate(map):
            print('To', index, 'Mapped', mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0],
                    self.file.shape[1], self.file.shape[3], self.file.shape[4])
                    )
            else:
                emptyfile[:, :, index, :, :] = self.file[:, :,
                    mappedchannel, :, :]
        print('Returned colormap shape', emptyfile.shape)
        return emptyfile

    def checkDimensions(self, file):
        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape
                [3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile
        assert self.file.shape[2] == 3, 'File Dimensions are wrong'
        return self.file

    def getFile(self):
        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
        return self.mappedfile

    def getMeta(self):
        return self.meta

    def readMeta(self):
        self.meta.run()
        pass

<mask token>


class BioMeta(object):
    <mask token>
    <mask token>
    <mask token>

    def intializeFromTiff(self):
        self.date = '1.3.91'

    def run(self):
        image = self.allmetadata[self.series]
        try:
            print(int(image.find('Pixels').attrs['SizeT']))
            self.date = str(image.find('AcquisitionDate').contents[0]
                ) if image.find('AcquisitionDate') is not None else 'NOT-SET'
            self.sizex = int(image.find('Pixels').attrs['SizeX']
                ) if image.find('Pixels').attrs['SizeX'] is not None else 0
            self.sizey = int(image.find('Pixels').attrs['SizeY']
                ) if image.find('Pixels').attrs['SizeY'] is not None else 0
            self.sizez = int(image.find('Pixels').attrs['SizeZ']
                ) if image.find('Pixels').attrs['SizeZ'] is not None else 0
            self.frames = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizet = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizec = int(image.find('Pixels').attrs['SizeC']
                ) if image.find('Pixels').attrs['SizeC'] is not None else 0
            self.physicalsizex = float(image.find('Pixels').attrs[
                'PhysicalSizeX']) if image.find('Pixels').attrs['PhysicalSizeX'
                ] is not None else 1
            self.physicalsizey = float(image.find('Pixels').attrs[
                'PhysicalSizeY']) if image.find('Pixels').attrs['PhysicalSizeY'
                ] is not None else 1
            self.physicalsizexunit = image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] is not None else 'Pixels'
            self.physicalsizeyunit = image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] is not None else 'Pixels'
        except:
            print('ITS NOT A VALID BIOIMAGEFILE')
        finally:
            return self
    <mask token>
    <mask token>
    <mask token>

    def getDirName(self):
        return 'AIS' + self.getFileName()

    def getFileName(self):
        return self.filepath.split('/')[-1].split('.')[0]
    <mask token>


class BioImageFile(object):

    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        javabridge.start_vm(class_path=bioformats.JARS)
        self.meta = BioMeta(filepath=filepath, standalone=False)
        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c
        self.debug = debug
        self.series = 0
        self.setz = 0
        self.shape = 0, 0, 0
        self.bioshape = 0, 0, 0

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True
        self.readMeta()
        self.readFile()
        return self

    def getImage(self, z=0, t=0):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        image = self.file[:, :, :, z, t]
        import scipy.misc
        cvimg = scipy.misc.toimage(image)
        img = np.array(cvimg)
        return img

    def getChannel(self, c=0, z=0, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, c, z, t]

    def getVideo(self, z=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self, start, end, t=0):
        print('Slized Stack', start, end)
        file = self.getFile()
        return file[:, :, :, start:end, t]

    def readFile(self):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.
            sizec, self.meta.sizez, self.meta.sizet))
        print('Channels:', self.meta.sizec)
        print('T-Size:', self.meta.sizet)
        print('Z-Size:', self.meta.sizez)
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True
            ) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):
                        im1 = reader.read(c=c, z=z, t=t, series=self.series,
                            rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if im1.shape[2] == 3:
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if self.meta.sizex == im2.shape[1
                            ] and self.meta.sizey == im2.shape[0
                            ] and not self.meta.sizex == self.meta.sizey:
                            im3 = im2.transpose()
                        else:
                            im3 = im2
                        self.file[:, :, c, z, t] = im3

    def colorMap(self, map):
        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
            self.file.shape[3], self.file.shape[4]))
        if len(map) != self.file.shape[2]:
            print('Less then 3 Channels, try different mapping')
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
                self.file.shape[3], self.file.shape[4]))
        for index, mappedchannel in enumerate(map):
            print('To', index, 'Mapped', mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0],
                    self.file.shape[1], self.file.shape[3], self.file.shape[4])
                    )
            else:
                emptyfile[:, :, index, :, :] = self.file[:, :,
                    mappedchannel, :, :]
        print('Returned colormap shape', emptyfile.shape)
        return emptyfile

    def checkDimensions(self, file):
        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape
                [3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile
        assert self.file.shape[2] == 3, 'File Dimensions are wrong'
        return self.file

    def getFile(self):
        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
        return self.mappedfile

    def getMeta(self):
        return self.meta

    def readMeta(self):
        self.meta.run()
        pass

<mask token>


class BioMeta(object):

    def __init__(self, filepath, standalone=True, series=0):
        self.filepath = filepath
        self.date = 0
        self.sizex = 0
        self.sizey = 0
        self.sizez = 0
        self.frames = 0
        self.sizet = 0
        self.sizec = 3
        self.series = 0
        self.physicalsizex = 1
        self.physicalsizey = 1
        self.physicalsizexunit = 'mm'
        self.physicalsizeyunit = 'mm'
        if standalone:
            javabridge.start_vm(class_path=bioformats.JARS)
        try:
            self.metadata_unparsed = bioformats.get_omexml_metadata(filepath)
            self.metadata = BeautifulSoup(self.metadata_unparsed, 'xml')
            self.setSeries(series)
            self.query_metadata()
        except:
            raise Exception(
                'BioMeta needs to be run in standalone Mode to initialize Javabridge'
                )
        finally:
            logging.info('BioMeta parsed')

    def getSeriesCount(self):
        return self.seriesamount
    <mask token>

    def intializeFromTiff(self):
        self.date = '1.3.91'

    def run(self):
        image = self.allmetadata[self.series]
        try:
            print(int(image.find('Pixels').attrs['SizeT']))
            self.date = str(image.find('AcquisitionDate').contents[0]
                ) if image.find('AcquisitionDate') is not None else 'NOT-SET'
            self.sizex = int(image.find('Pixels').attrs['SizeX']
                ) if image.find('Pixels').attrs['SizeX'] is not None else 0
            self.sizey = int(image.find('Pixels').attrs['SizeY']
                ) if image.find('Pixels').attrs['SizeY'] is not None else 0
            self.sizez = int(image.find('Pixels').attrs['SizeZ']
                ) if image.find('Pixels').attrs['SizeZ'] is not None else 0
            self.frames = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizet = int(image.find('Pixels').attrs['SizeT']
                ) if image.find('Pixels').attrs['SizeT'] is not None else 0
            self.sizec = int(image.find('Pixels').attrs['SizeC']
                ) if image.find('Pixels').attrs['SizeC'] is not None else 0
            self.physicalsizex = float(image.find('Pixels').attrs[
                'PhysicalSizeX']) if image.find('Pixels').attrs['PhysicalSizeX'
                ] is not None else 1
            self.physicalsizey = float(image.find('Pixels').attrs[
                'PhysicalSizeY']) if image.find('Pixels').attrs['PhysicalSizeY'
                ] is not None else 1
            self.physicalsizexunit = image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeXUnit'] is not None else 'Pixels'
            self.physicalsizeyunit = image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] if image.find('Pixels').attrs[
                'PhysicalSizeYUnit'] is not None else 'Pixels'
        except:
            print('ITS NOT A VALID BIOIMAGEFILE')
        finally:
            return self
    <mask token>

    def getChannelNames(self):
        channelexplain = Global.colorReadableMap
        try:
            channellist = [(i.attrs['Name'] + ' (' + channelexplain[index] +
                ')') for index, i in enumerate(self.allmetadata[self.series
                ].findAll('Channel'))]
            return channellist
        except:
            channellist = [channelexplain[i] for i in range(self.sizec)]
            return channellist

    def getSeriesName(self):
        try:
            seriesname = self.allmetadata[self.series].attrs['Name']
        except:
            seriesname = 'Not Specified'
        return seriesname

    def getDirName(self):
        return 'AIS' + self.getFileName()

    def getFileName(self):
        return self.filepath.split('/')[-1].split('.')[0]

    def __str__(self):
        return str(self.allmetadata[self.series])


class BioImageFile(object):

    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        javabridge.start_vm(class_path=bioformats.JARS)
        self.meta = BioMeta(filepath=filepath, standalone=False)
        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c
        self.debug = debug
        self.series = 0
        self.setz = 0
        self.shape = 0, 0, 0
        self.bioshape = 0, 0, 0

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True
        self.readMeta()
        self.readFile()
        return self

    def getImage(self, z=0, t=0):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        image = self.file[:, :, :, z, t]
        import scipy.misc
        cvimg = scipy.misc.toimage(image)
        img = np.array(cvimg)
        return img

    def getChannel(self, c=0, z=0, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, c, z, t]

    def getVideo(self, z=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert self.ran == True, 'BioimageFile has no been instatiated'
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self, start, end, t=0):
        print('Slized Stack', start, end)
        file = self.getFile()
        return file[:, :, :, start:end, t]

    def readFile(self):
        assert self.ran is True, 'BioimageFile has no been instatiated'
        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.
            sizec, self.meta.sizez, self.meta.sizet))
        print('Channels:', self.meta.sizec)
        print('T-Size:', self.meta.sizet)
        print('Z-Size:', self.meta.sizez)
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True
            ) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):
                        im1 = reader.read(c=c, z=z, t=t, series=self.series,
                            rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if im1.shape[2] == 3:
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if self.meta.sizex == im2.shape[1
                            ] and self.meta.sizey == im2.shape[0
                            ] and not self.meta.sizex == self.meta.sizey:
                            im3 = im2.transpose()
                        else:
                            im3 = im2
                        self.file[:, :, c, z, t] = im3

    def colorMap(self, map):
        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
            self.file.shape[3], self.file.shape[4]))
        if len(map) != self.file.shape[2]:
            print('Less then 3 Channels, try different mapping')
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3,
                self.file.shape[3], self.file.shape[4]))
        for index, mappedchannel in enumerate(map):
            print('To', index, 'Mapped', mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0],
                    self.file.shape[1], self.file.shape[3], self.file.shape[4])
                    )
            else:
                emptyfile[:, :, index, :, :] = self.file[:, :,
                    mappedchannel, :, :]
        print('Returned colormap shape', emptyfile.shape)
        return emptyfile

    def checkDimensions(self, file):
        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape
                [3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile
        assert self.file.shape[2] == 3, 'File Dimensions are wrong'
        return self.file

    def getFile(self):
        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
        return self.mappedfile

    def getMeta(self):
        return self.meta

    def readMeta(self):
        self.meta.run()
        pass

#  This file is part of AISelect.

#  AISelect is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.

#  AISelect is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with AISelect.  If not, see <http://www.gnu.org/licenses/>.


import math, bioformats
import numpy as np
import javabridge
from bs4 import BeautifulSoup
import logging

from settings import Global


class BioMeta(object):
    def __init__(self, filepath, standalone=True, series=0):

        self.filepath = filepath
        self.date = 0
        self.sizex = 0
        self.sizey = 0
        self.sizez = 0
        self.frames = 0
        self.sizet = 0
        self.sizec = 3
        self.series = 0

        # self.physicalsizet = float(image.find("Pixels").attrs[""])
        self.physicalsizex = 1
        self.physicalsizey = 1
        self.physicalsizexunit = "mm"
        self.physicalsizeyunit = "mm"

        if standalone: javabridge.start_vm(class_path=bioformats.JARS)

        try:
            self.metadata_unparsed = bioformats.get_omexml_metadata(filepath)
            self.metadata = BeautifulSoup(self.metadata_unparsed, "xml")
            # defaultseries
            self.setSeries(series)
            self.query_metadata()
        except:
            raise Exception("BioMeta needs to be run in standalone Mode to initialize Javabridge")
        finally:
            logging.info("BioMeta parsed")

    def getSeriesCount(self):
        return self.seriesamount

    def setSeries(self, it):
        self.series = it
        return self

    def intializeFromTiff(self):

        self.date = "1.3.91"


    def run(self):
        image = self.allmetadata[self.series]
        try:
            print(int(image.find("Pixels").attrs["SizeT"]))
            self.date = str(image.find("AcquisitionDate").contents[0]) if image.find("AcquisitionDate") is not None else "NOT-SET"
            self.sizex = int(image.find("Pixels").attrs["SizeX"]) if image.find("Pixels").attrs["SizeX"] is not None else 0
            self.sizey = int(image.find("Pixels").attrs["SizeY"]) if image.find("Pixels").attrs["SizeY"] is not None else 0
            self.sizez = int(image.find("Pixels").attrs["SizeZ"]) if image.find("Pixels").attrs["SizeZ"] is not None else 0
            self.frames = int(image.find("Pixels").attrs["SizeT"]) if image.find("Pixels").attrs["SizeT"] is not None else 0
            self.sizet = int(image.find("Pixels").attrs["SizeT"]) if image.find("Pixels").attrs["SizeT"] is not None else 0
            self.sizec = int(image.find("Pixels").attrs["SizeC"]) if image.find("Pixels").attrs["SizeC"] is not None else 0

            # self.physicalsizet = float(image.find("Pixels").attrs[""])
            self.physicalsizex = float(image.find("Pixels").attrs["PhysicalSizeX"]) if image.find("Pixels").attrs["PhysicalSizeX"] is not None else 1
            self.physicalsizey = float(image.find("Pixels").attrs["PhysicalSizeY"]) if image.find("Pixels").attrs["PhysicalSizeY"] is not None else 1
            self.physicalsizexunit = image.find("Pixels").attrs["PhysicalSizeXUnit"] if image.find("Pixels").attrs["PhysicalSizeXUnit"] is not None else "Pixels"
            self.physicalsizeyunit = image.find("Pixels").attrs["PhysicalSizeYUnit"] if image.find("Pixels").attrs["PhysicalSizeYUnit"] is not None else "Pixels"
        except:
            print("ITS NOT A VALID BIOIMAGEFILE")
        finally:
            return self

    def query_metadata(self):
        self.allmetadata = self.metadata.findAll("Image")
        self.seriesamount = len(self.allmetadata)

    def getChannelNames(self):

        channelexplain = Global.colorReadableMap
        try:
            channellist = [i.attrs["Name"]+" (" + channelexplain[index]+ ")" for index,i in enumerate(self.allmetadata[self.series].findAll("Channel"))]
            return channellist
        except:
            channellist = [channelexplain[i] for i in range(self.sizec)]
            return channellist

    def getSeriesName(self):
        try:
            seriesname = self.allmetadata[self.series].attrs["Name"]
        except:
            seriesname = "Not Specified"
        return seriesname

    def getDirName(self):
        return "AIS" + self.getFileName()

    def getFileName(self):
        return self.filepath.split("/")[-1].split(".")[0]

    def __str__(self):
        return str(self.allmetadata[self.series])


class BioImageFile(object):
    def __init__(self, filepath, z=None, c=None, channels=None, debug=False):
        # Initialize JAVABRIDGE
        javabridge.start_vm(class_path=bioformats.JARS)

        self.meta = BioMeta(filepath=filepath, standalone=False)

        self.filepath = filepath
        self.layer = z
        self.channels = None
        self.c = c

        # STANDARD SETTINGS HERE
        self.debug = debug
        self.series = 0
        self.setz = 0

        #META
        self.shape = (0,0,0) #TODO: setRoutines
        self.bioshape = (0,0,0)

    def setSeries(self, series=0):
        self.series = series
        self.meta.setSeries(series)
        self.meta.run()
        return self

    def run(self):
        self.ran = True

        # Must be run before Picture is correctly processed
        self.readMeta()
        self.readFile()

        return self

    def getImage(self, z=0, t=0):
        assert (self.ran is True), "BioimageFile has no been instatiated"
        #TODO: THIs is to dirty and needs invastigating
        image = self.file[:, :, :, z, t]
        import scipy.misc
        cvimg = scipy.misc.toimage(image)
        img = np.array(cvimg)
        return img

    def getChannel(self, c=0, z=0, t=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        return self.file[:, :, c, z, t]

    def getVideo(self, z=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        return self.file[:, :, :, z, :]

    def getZStack(self, t=0):
        assert (self.ran == True), "BioimageFile has no been instatiated"
        file = self.getFile()
        return file[:, :, :, :, t]

    def getZSize(self):
        return self.meta.sizez

    def getSlicedStack(self,start,end, t=0):
        print("Slized Stack",start,end)
        file = self.getFile()
        return file[:,:,:,start:end,t]


    def readFile(self):

        assert (self.ran is True), "BioimageFile has no been instatiated"

        self.file = np.zeros((self.meta.sizex, self.meta.sizey, self.meta.sizec, self.meta.sizez, self.meta.sizet))
        print("Channels:", self.meta.sizec)
        print("T-Size:",self.meta.sizet)
        print("Z-Size:",self.meta.sizez)
        # Debug settings
        tsize = self.meta.sizet if not self.debug else 20
        print(tsize)
        with bioformats.ImageReader(self.filepath, perform_init=True) as reader:
            for c in range(self.meta.sizec):
                for z in range(self.meta.sizez):
                    for t in range(tsize):

                        # bioformats appears to swap axes for tif images and read all three channels at a time for RGB
                        im1 = reader.read(c=c, z=z, t=t, series=self.series, rescale=True, channel_names=None)
                        if im1.ndim == 3:
                            if (im1.shape[2] == 3):
                                # Three channels are red
                                im2 = im1[:, :, c]
                            else:
                                im2 = im1
                        else:
                            im2 = im1
                        if (self.meta.sizex == im2.shape[1]) and (self.meta.sizey == im2.shape[0]) and not self.meta.sizex == self.meta.sizey:
                            # x and y are swapped
                            #logging.warning("Image might be transposed. Not Swapping")
                            #im3 = im2.transpose()
                            im3 = im2.transpose()
                        else:
                            im3 = im2


                        self.file[:, :, c, z, t] = im3



        #needs to check if image is in rgb format to display


    def colorMap(self,map):

        emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3, self.file.shape[3], self.file.shape[4]))

        if len(map) != self.file.shape[2]:
            print("Less then 3 Channels, try different mapping")
            map = map[:self.file.shape[2]]
            emptyfile = np.zeros((self.file.shape[0], self.file.shape[1], 3, self.file.shape[3], self.file.shape[4]))

        for index, mappedchannel in enumerate(map):
            print( "To", index, "Mapped", mappedchannel)
            if mappedchannel >= self.file.shape[2]:
                emptyfile[:, :, index, :, :] = np.zeros((self.file.shape[0], self.file.shape[1], self.file.shape[3], self.file.shape[4]))
            else:
                emptyfile[:,:,index,:,:] = self.file[:,:,mappedchannel,:,:]

        print("Returned colormap shape", emptyfile.shape)
        return emptyfile

    def checkDimensions(self,file):
        # unnecessary step

        if file.shape[2] != 3:
            newfile = np.zeros((file.shape[0], file.shape[1], 3, file.shape[3], file.shape[4]))
            newfile[:, :, 1:3, :, :] = file
            file = newfile


        assert self.file.shape[2] == 3, "File Dimensions are wrong"

        return self.file


    def getFile(self):

        print(Global.colorMap)
        self.mappedfile = self.colorMap(Global.colorMap)
       # self.checkedfile = self.checkDimensions(self.mappedfile)

        return self.mappedfile


    def getMeta(self):

        return self.meta

    def readMeta(self):
        self.meta.run()
        pass