ResMap.py

"""
ResMap is a Python (NumPy/SciPy) application with a Tkinter GUI.
It is a software package for computing the local resolution of 3D
density maps studied in structural biology, primarily electron
cryo-microscopy (cryo-EM).

Please find the manual at http://resmap.sourceforge.net

If you use ResMap in your work, please consider citing us:

A. Kucukelbir, F.J. Sigworth, and H.D. Tagare, Quantifying the
Local Resolution of Cryo-EM Density Maps, Nature Methods.
Volume 11, Issue 1, Pages 63-65, 2014.

This package is released under the Creative Commons
Attribution-NonCommercial-NoDerivs CC BY-NC-ND License
(http://creativecommons.org/licenses/by-nc-nd/3.0/)

Usage:
  ResMap.py [(--noguiSingle INPUT)] [--vxSize=VXSIZE]
            [--pVal=PVAL]
            [--minRes=MINRES] [--maxRes=MAXRES] [--stepRes=STEPRES]
            [--maskVol=MASKVOL]
            [--vis2D] [--launchChimera] [--noiseDiag]
  ResMap.py [(--noguiSplit INPUT1 INPUT2)] [--vxSize=VXSIZE]
            [--pVal=PVAL]
            [--minRes=MINRES] [--maxRes=MAXRES] [--stepRes=STEPRES]
            [--maskVol=MASKVOL]
            [--vis2D] [--launchChimera] [--noiseDiag]

NOTE: INPUT(s) is/are mandatory

Arguments:
  INPUT(s)            Input volume(s) in MRC format

Options:
  --noguiSingle       Run ResMap for Single Volumes in command-line mode
  --noguiSplit        Run ResMap for Split Volumes in command-line mode
  --vxSize=VXSIZE     Voxel size of input map (A) [default: 0.0]
  --pVal=PVAL         P-value for likelihood ratio test [default: 0.05]
  --minRes=MINRES     Minimum resolution (A) [default: 0.0]
  --maxRes=MAXRES     Maximum resolution (A) [default: 0.0]
  --stepRes=STEPRES   Step size (A) [default: 1.0]
  --maskVol=MASKVOL   Mask volume
  --vis2D             Output 2D visualization
  --launchChimera     Attempt to launch Chimera after execution
  --noiseDiag         Run and show noise diagnostics
  -h --help           Show this help message and exit
  --version           Show version.

"""




import os
from docopt import docopt
from sys import exit

from ResMap_fileIO import *
from ResMap_algorithm import ResMap_algorithm

class ResMapApp(object):

    """GUI Tkinter class for ResMap"""

    def __init__(self, parent):

        # General Settings
        self.parent = parent
        self.parent.title("ResMap (Local Resolution) v" + version)
        self.parent.option_add('*tearOff', False)

        self.myStyle = ttk.Style()
        self.myStyle.configure('ResMap.TButton', foreground='red4',
                                font='Helvetica 16 bold')


        ## MENUBAR
        # Create menubar frame
        self.menubar = ttk.Frame(parent)
        self.menubar.pack(side=tk.TOP, fill=tk.X)

        # Create Help menubutton"path":
        self.mb_help = ttk.Menubutton(self.menubar, text="Help")
        self.mb_help.pack(side=tk.RIGHT)

        # Create Help menu
        self.helpMenu = tk.Menu(self.mb_help)
        self.helpMenu.add_command(label="Documentation",
                                  command=self.showDocumentation)
        self.helpMenu.add_command(label="About ResMap",
                                  command=self.showAbout)

        # Attach the Help menu to the Help menubutton
        self.mb_help.config(menu = self.helpMenu)


        ## MASTER FRAME
        # Create master frame that holds everything
        self.masterframe = ttk.Frame(parent)
        self.masterframe.pack()

        # Create notebook
        self.nb = ttk.Notebook(self.masterframe, style='ResMap.TNotebook')
        self.nb.enable_traversal() # allow for keyboard bindings
        self.nb.pack()


        ## GLOBAL VARIABLES FOR BOTH NOTEBOOK FRAMES
        # Create Tk variables
        self.graphicalOutput  = tk.IntVar(value=1)
        self.chimeraLaunch    = tk.IntVar()
        self.noiseDiagnostics = tk.IntVar()
        self.volFileName      = tk.StringVar()
        self.volFileName1     = tk.StringVar()
        self.volFileName2     = tk.StringVar()
        self.voxelSize        = tk.StringVar(value="Auto")
        self.alphaValue       = tk.StringVar(value="0.05")
        self.minRes           = tk.StringVar(value="0.0")
        self.maxRes           = tk.StringVar(value="0.0")
        self.stepRes          = tk.StringVar(value="1.0")
        self.maskFileName     = tk.StringVar(value=("None; "
            "ResMap will automatically compute a mask. Load File to override."))

        ## SINGLE VOLUME FRAME
        # Create single volume input frame
        self.mainframe = ttk.Frame(self.nb)

        self.mainframe.grid(column=0, row=0, sticky=(tk.N, tk.W, tk.E, tk.S))
        self.mainframe.columnconfigure(0, weight=1)
        self.mainframe.rowconfigure(0, weight=1)

        self.nb.add(self.mainframe, text='Single Volume Input',
                    underline=0, padding=10)

        # ROW 0
        ttk.Label(self.mainframe, text="Required Inputs", font = "Helvetica 14 bold").grid(column=1, row=0, columnspan=10, sticky=tk.W)

        # ROW 1
        ttk.Label(self.mainframe, text="Volume:").grid(column=1, row=1, sticky=tk.E)
        ttk.Entry(self.mainframe, width=100, textvariable=self.volFileName).grid(column=2, columnspan=10, row=1, sticky=(tk.W, tk.E))
        ttk.Button(self.mainframe, text="Load", command=(lambda: self.load_file(self.volFileName))).grid(column=12, row=1, sticky=tk.W)

        # ROW 2
        ttk.Label(self.mainframe, text="Voxel Size:").grid(column=1, row=2, sticky=tk.E)
        ttk.Entry(self.mainframe, width=5, textvariable=self.voxelSize, foreground="gray").grid(column=2, row=2, sticky=tk.W)
        ttk.Label(self.mainframe, text="Angstrom/voxel (default: algorithm will read value from MRC header)").grid(column=3, row=2, sticky=tk.W)

        # ROW 3
        ttk.Label(self.mainframe, text="Optional Inputs", font = "Helvetica 14 bold").grid(column=1, row=3, columnspan=8, sticky=tk.W)

        # ROW 4
        ttk.Label(self.mainframe, text="Step Size:").grid(column=1, row=4, sticky=tk.E)
        ttk.Entry(self.mainframe, width=5, textvariable=self.stepRes).grid(column=2, row=4, sticky=tk.W)
        ttk.Label(self.mainframe, text="in Angstroms (min: 0.25, default: 1.0)").grid(column=3, row=4, sticky=tk.W)

        # ROW 5
        ttk.Label(self.mainframe, text="Min Resolution:").grid(column=1, row=5, sticky=tk.E)
        ttk.Entry(self.mainframe, width=5, textvariable=self.minRes).grid(column=2, row=5, sticky=tk.W)
        ttk.Label(self.mainframe, text="in Angstroms (default: algorithm will start at just above 2*voxelSize)").grid(column=3, row=5, sticky=tk.W)

        # ROW 6
        ttk.Label(self.mainframe, text="Max Resolution:").grid(column=1, row=6, sticky=tk.E)
        ttk.Entry(self.mainframe, width=5, textvariable=self.maxRes).grid(column=2, row=6, sticky=tk.W)
        ttk.Label(self.mainframe, text="in Angstroms (default: algorithm will stop at around 4*voxelSize)").grid(column=3, row=6, sticky=tk.W)

        # ROW 7
        ttk.Label(self.mainframe, text="Confidence Level:").grid(column=1, row=7, sticky=tk.E)
        ttk.Entry(self.mainframe, width=5, textvariable=self.alphaValue).grid(column=2, row=7, sticky=tk.W)
        ttk.Label(self.mainframe, text="usually between [0.01, 0.05]").grid(column=3, row=7, sticky=tk.W)

        # ROW 8
        ttk.Label(self.mainframe, text="Mask Volume:").grid(column=1, row=8, sticky=tk.E)
        ttk.Entry(self.mainframe, width=100, textvariable=self.maskFileName, foreground="gray").grid(column=2, columnspan=10, row=8, sticky=(tk.W, tk.E))
        ttk.Button(self.mainframe, text="Load", command=(lambda: self.load_file(self.maskFileName))).grid(column=12, row=8, sticky=tk.W)

        # ROW 9
        ttk.Label(self.mainframe, text="Visualization Options:").grid(column=1, row=9, sticky=tk.E)
        ttk.Checkbutton(self.mainframe, text="2D Result Visualization (ResMap)", variable=self.graphicalOutput).grid(column=2, row=9, columnspan=2, sticky=tk.W)

        # ROW 10
        ttk.Checkbutton(self.mainframe, text="3D Result Visualization (UCSF Chimera)", variable=self.chimeraLaunch).grid(column=2, row=10, columnspan=2 , sticky=tk.W)

        # # ROW 12
        # ttk.Label(self.mainframe, text="Diagnostics Options:").grid(column=1, row=12, sticky=tk.E)
        # ttk.Checkbutton(self.mainframe, text="Display Noise Diagnostics (ResMap)", variable=self.noiseDiagnostics).grid(column=2, row=12, columnspan=2, sticky=tk.W)

        # ROW 13
        ttk.Button(self.mainframe, text="Check Inputs and RUN", style='ResMap.TButton', command=self.checkInputsAndRun).grid(column=9, columnspan=4, row=13, sticky=tk.E)

        # Setup grid with padding
        for child in self.mainframe.winfo_children(): child.grid_configure(padx=5, pady=5)

        self.parent.bind("<Return>",self.checkInputsAndRun)

        ## SPLIT VOLUME FRAME
        # Create split volume input frame
        self.splitframe = ttk.Frame(self.nb)

        self.splitframe.grid(column=0, row=0, sticky=(tk.N, tk.W, tk.E, tk.S))
        self.splitframe.columnconfigure(0, weight=1)
        self.splitframe.rowconfigure(   0, weight=1)

        self.nb.add(self.splitframe, text='Split Volume Input', underline=0, padding=10)

        # ROW 0
        ttk.Label(self.splitframe, text="Required Inputs", font = "Helvetica 14 bold").grid(column=1, row=0, columnspan=10, sticky=tk.W)

        # ROW 1
        ttk.Label(self.splitframe, text="Split Volume 1:").grid(column=1, row=1, sticky=tk.E)
        ttk.Entry(self.splitframe, width=100, textvariable=self.volFileName1).grid(column=2, columnspan=10, row=1, sticky=(tk.W, tk.E))

        # ROW 2
        ttk.Label(self.splitframe, text="Split Volume 2:").grid(column=1, row=2, sticky=tk.E)
        ttk.Entry(self.splitframe, width=100, textvariable=self.volFileName2).grid(column=2, columnspan=10, row=2, sticky=(tk.W, tk.E))
        ttk.Button(self.splitframe, text="Load Both", command=(lambda: self.load_files(self.volFileName1, self.volFileName2))).grid(column=12, row=2, sticky=tk.W)

        # ROW 3
        ttk.Label(self.splitframe, text="Voxel Size:").grid(column=1, row=3, sticky=tk.E)
        ttk.Entry(self.splitframe, width=5, textvariable=self.voxelSize, foreground="gray").grid(column=2, row=3, sticky=tk.W)
        ttk.Label(self.splitframe, text="Angstrom/voxel (default: algorithm will read value from MRC header)").grid(column=3, row=3, sticky=tk.W)

        # ROW 4
        ttk.Label(self.splitframe, text="Optional Inputs", font = "Helvetica 14 bold").grid(column=1, row=4, columnspan=8, sticky=tk.W)

        # ROW 5
        ttk.Label(self.splitframe, text="Step Size:").grid(column=1, row=5, sticky=tk.E)
        ttk.Entry(self.splitframe, width=5, textvariable=self.stepRes).grid(column=2, row=5, sticky=tk.W)
        ttk.Label(self.splitframe, text="in Angstroms (min: 0.25, default: 1.0)").grid(column=3, row=5, sticky=tk.W)

        # ROW 6
        ttk.Label(self.splitframe, text="Min Resolution:").grid(column=1, row=6, sticky=tk.E)
        ttk.Entry(self.splitframe, width=5, textvariable=self.minRes).grid(column=2, row=6, sticky=tk.W)
        ttk.Label(self.splitframe, text="in Angstroms (default: algorithm will start at just above 2*voxelSize)").grid(column=3, row=6, sticky=tk.W)

        # ROW 7
        ttk.Label(self.splitframe, text="Max Resolution:").grid(column=1, row=7, sticky=tk.E)
        ttk.Entry(self.splitframe, width=5, textvariable=self.maxRes).grid(column=2, row=7, sticky=tk.W)
        ttk.Label(self.splitframe, text="in Angstroms (default: algorithm will stop at around 4*voxelSize)").grid(column=3, row=7, sticky=tk.W)

        # ROW 8
        ttk.Label(self.splitframe, text="Confidence Level:").grid(column=1, row=8, sticky=tk.E)
        ttk.Entry(self.splitframe, width=5, textvariable=self.alphaValue).grid(column=2, row=8, sticky=tk.W)
        ttk.Label(self.splitframe, text="usually between [0.01, 0.05]").grid(column=3, row=8, sticky=tk.W)

        # ROW 9
        ttk.Label(self.splitframe, text="Mask Volume:").grid(column=1, row=9, sticky=tk.E)
        ttk.Entry(self.splitframe, width=100, textvariable=self.maskFileName, foreground="gray").grid(column=2, columnspan=10, row=9, sticky=(tk.W, tk.E))
        ttk.Button(self.splitframe, text="Load", command=(lambda: self.load_file(self.maskFileName))).grid(column=12, row=9, sticky=tk.W)

        # ROW 10
        ttk.Label(self.splitframe, text="Visualization Options:").grid(column=1, row=10, sticky=tk.E)
        ttk.Checkbutton(self.splitframe, text="2D Result Visualization (ResMap)", variable=self.graphicalOutput).grid(column=2, row=10, columnspan=2, sticky=tk.W)

        # ROW 11
        ttk.Checkbutton(self.splitframe, text="3D Result Visualization (UCSF Chimera)", variable=self.chimeraLaunch).grid(column=2, row=11, columnspan=2, sticky=tk.W)

        # # ROW 12
        # ttk.Label(self.splitframe, text="Diagnostics Options:").grid(column=1, row=12, sticky=tk.E)
        # ttk.Checkbutton(self.splitframe, text="Display Noise Diagnostics (ResMap)", variable=self.noiseDiagnostics).grid(column=2, row=12, columnspan=2, sticky=tk.W)

        # ROW 13
        ttk.Button(self.splitframe, text="Check Inputs and RUN", style='ResMap.TButton', command=self.checkInputsAndRun).grid(column=9, columnspan=4, row=13, sticky=tk.E)

        # Setup grid with padding
        for child in self.splitframe.winfo_children(): child.grid_configure(padx=5, pady=5)

    def load_file(self, fileNameStringVar):
        options =  {}
        # options['filetypes'] = [ ("All files", ".*"), ("MRC map", ".map,.mrc") ]      # THIS SEEMS BUGGY...
        options['title'] = "ResMap - Select data file"
        fname = askopenfilename(**options)
        if fname:
            try:
                fileNameStringVar.set(fname)
            except:                     # <- naked except is a bad idea
                showerror("Open Source File", "Failed to read file\n'%s'" % fname)
            return

    def load_files(self, fileNameStringVar1, fileNameStringVar2):
        options =  {}
        options['title'] = "ResMap - Select data file"
        fname = askopenfilenames(**options)
        if isinstance( fname, tuple ):
            try:
                fileNameStringVar1.set(fname[0])
                fileNameStringVar2.set(fname[1])
            except:                     # <- naked except is a bad idea
                showerror("Open Source Files", "Failed to read files\n'%s'" % fname)
            return
        if isinstance( fname, unicode ):
            try:
                fileNameStringVar1.set(fname.partition(' ')[0])
                fileNameStringVar2.set(fname.partition(' ')[2])
            except:                     # <- naked except is a bad idea
                showerror("Open Source Files", "Failed to read files\n'%s'" % fname)
            return

    def checkInputsAndRun(self,*args):

        # Find which tab the button was pressed from
        if self.nb.index(self.nb.select()) == 0:
            singleVolumeTab = True
        else:
            singleVolumeTab = False

        if singleVolumeTab:
            # Check single volume file name and try loading MRC file
            if self.volFileName.get() == "":
                showerror("Check Inputs", "'volFileName' is not set. Please select a MRC volume to analyze.")
                return
            else:
                try:
                    inputFileName = self.volFileName.get()
                    data = MRC_Data(inputFileName,'ccp4')
                except:
                    showerror("Check Inputs", "The MRC volume could not be read.")
                    return
        else:
            # Check split volume file names and try loading MRC files
            if self.volFileName1.get() == "":
                showerror("Check Inputs", "'volFileName1' is not set. Please select a MRC volume to analyze.")
                return
            else:
                try:
                    inputFileName1 = self.volFileName1.get()
                    data1 = MRC_Data(inputFileName1,'ccp4')
                except:
                    showerror("Check Inputs", "The MRC volume could not be read.")
                    return

            if self.volFileName2.get() == "":
                showerror("Check Inputs", "'volFileName2' is not set. Please select a MRC volume to analyze.")
                return
            else:
                try:
                    inputFileName2 = self.volFileName2.get()
                    data2 = MRC_Data(inputFileName2,'ccp4')
                except:
                    showerror("Check Inputs", "The MRC volume could not be read.")
                    return

        # Check voxel size
        if self.voxelSize.get() == "":
            showerror("Check Inputs", "'voxelSize' is not set. Please input a voxel size in Angstroms.")
            return
        elif self.voxelSize.get().split(';',1)[0] == "Auto":
            try:
                if singleVolumeTab:
                    vxSize = float(data.data_step[0])
                else:
                    vxSize = float(data1.data_step[0])
            except ValueError:
                showerror("Check Inputs", "'voxelSize' cannot be read from the MRC file. Please input a valid voxel size in Angstroms.")
                return
        else:
            try:
                vxSize = float(self.voxelSize.get())
            except ValueError:
                showerror("Check Inputs", "'voxelSize' is not a valid number. Please input a valid voxel size in Angstroms.")
                return

        if vxSize <= 0.0:
            showerror("Check Inputs", "'voxelSize' is not a positive number. Please input a positive voxel size in Angstroms.")
            return

        # Check confidence level
        if self.alphaValue.get() == "":
            showerror("Check Inputs", "'alphaValue' is not set. Please input a valid confidence level.")
            return
        else:
            try:
                pValue = float(self.alphaValue.get())
            except ValueError:
                showerror("Check Inputs", "'alphaValue' is not a valid number. Please input a valid confidence level.")
                return

            if pValue <= 0 or pValue > 0.05:
                showerror("Check Inputs", "'alphaValue' is outside of (0, 0.05]. Please input a valid confidence level.")
                return

        # Check min resolution
        if self.minRes.get() == "":
            showerror("Check Inputs", "'minRes' is not set. Please input a valid minimum resolution in Angstroms.")
            return
        else:
            try:
                minRes = float(self.minRes.get())
            except ValueError:
                showerror("Check Inputs", "'minRes' is not a valid number. Please input a valid minimum resolution in Angstroms.")
                return

            if minRes < 0.0:
                showerror("Check Inputs", "'minRes' is not a positive number. Please input a positive minimum resolution in Angstroms.")
                return

        # Check max resolution
        if self.maxRes.get() == "":
            showerror("Check Inputs", "'maxRes' is not set. Please input a valid maximum resolution in Angstroms.")
            return
        else:
            try:
                maxRes = float(self.maxRes.get())
            except ValueError:
                showerror("Check Inputs", "'maxRes' is not a valid number. Please input a valid maximum resolution in Angstroms.")
                return

            if maxRes < 0.0:
                showerror("Check Inputs", "'maxRes' is not a positive number. Please input a positive maximum resolution in Angstroms.")
                return

        # Check step size
        if self.stepRes.get() == "":
            showerror("Check Inputs", "'stepRes' is not set. Please input a valid step size in Angstroms.")
            return
        else:
            try:
                stepRes = float(self.stepRes.get())
            except ValueError:
                showerror("Check Inputs", "'stepRes' is not a valid number. Please input a valid step size in Angstroms.")
                return

            if stepRes < 0.25:
                showerror("Check Inputs", "'stepRes' is too small. Please input a step size greater than 0.25 in Angstroms.")
                return

        # Check mask file name and try loading MRC file
        if self.maskFileName.get() == "":
            showerror("Check Inputs", "'maskFileName' is not set. Please type (None;) without the parantheses.")
            return
        elif self.maskFileName.get().split(';',1)[0] == "None":
            dataMask = 0
        else:
            try:
                maskVolFileName = self.maskFileName.get()
                dataMask = MRC_Data(maskVolFileName,'ccp4')
            except:
                showerror("Check Inputs", "The MRC mask file could not be read.")
                return

        showinfo("ResMap","Inputs are all valid!\n\nPress OK to close GUI and RUN.\n\nCheck console for progress.")

        root.destroy()

        # Call ResMap
        if singleVolumeTab:
            ResMap_algorithm(
                    inputFileName    = inputFileName,
                    data             = data,
                    vxSize           = vxSize,
                    pValue           = pValue,
                    minRes           = minRes,
                    maxRes           = maxRes,
                    stepRes          = stepRes,
                    dataMask         = dataMask,
                    graphicalOutput  = self.graphicalOutput.get(),
                    chimeraLaunch    = self.chimeraLaunch.get(),
                    noiseDiagnostics = self.noiseDiagnostics.get(),
                 )
        else:
            ResMap_algorithm(
                    inputFileName1   = inputFileName1,
                    inputFileName2   = inputFileName2,
                    data1            = data1,
                    data2            = data2,
                    vxSize           = vxSize,
                    pValue           = pValue,
                    minRes           = minRes,
                    maxRes           = maxRes,
                    stepRes          = stepRes,
                    dataMask         = dataMask,
                    graphicalOutput  = self.graphicalOutput.get(),
                    chimeraLaunch    = self.chimeraLaunch.get(),
                    noiseDiagnostics = self.noiseDiagnostics.get(),
                 )

        raw_input("\n== DONE! ==\n\nPress any key or close window to EXIT.\n\n")

        return

    def showAbout(self):
        showinfo("About ResMap",
        ("This is ResMap v."+version+".\n\n"
         "If you use ResMap in your work, please cite the following paper:\n\n"
         "A. Kucukelbir, F.J. Sigworth, and H.D. Tagare, Quantifying the " \
         "Local Resolution of Cryo-EM Density Maps, Nature Methods. " \
         "Volume 11, Issue 1, Pages 63-65, 2014.\n\n"
         "This package is released under the Creative Commons " \
         "Attribution-NonCommercial-NoDerivs CC BY-NC-ND License " \
         "(http://creativecommons.org/licenses/by-nc-nd/3.0/)\n\n"
         "Please send comments, suggestions, and bug reports to " \
         "alpk@aya.yale.edu or hemant.tagare@yale.edu"))

    def showDocumentation(self):
        showinfo("ResMap Documentation",
            "Please download the manual at http://resmap.sourceforge.net")

if __name__ == '__main__':

    global version
    version = "1.1.5"

    args = docopt(__doc__, version=version)

    if args['--noguiSingle'] == False and args['--noguiSplit'] == False:

        # Create root window and initiate GUI interface
        import Tkinter as tk
        from tkFileDialog import askopenfilename
        from tkFileDialog import askopenfilenames
        from tkMessageBox import showerror
        from tkMessageBox import showinfo
        import ttk
        root = tk.Tk()
        resmapapp = ResMapApp(root)
        root.mainloop()

    else:

        if args['--noguiSingle'] == True:
            # INPUT
            #try:
            print("Reading ", args['INPUT'])
            data = MRC_Data(args['INPUT'],'ccp4')
            vxSize = float(data.data_step[0])
            #except:
            #    exit("The input volume (MRC/CCP4 format) could not be read.")

            # inputFileName
            inputFileName = os.path.normpath(os.path.join(os.getcwd(),args['INPUT']))
        elif args['--noguiSplit'] == True:
            # INPUT
            try:
                data1 = MRC_Data(args['INPUT1'],'ccp4')
                data2 = MRC_Data(args['INPUT2'],'ccp4')
                vxSize = float(data1.data_step[0])
            except:
                exit("The input volumes (MRC/CCP4 format) could not be read.")

            # inputFileName
            inputFileName1 = os.path.normpath(os.path.join(os.getcwd(),args['INPUT1']))
            inputFileName2 = os.path.normpath(os.path.join(os.getcwd(),args['INPUT2']))

        # --vxSize
        if float(args['--vxSize']) > 0.0:   # Only grab the vxSize if it is inputted
            try:
                vxSize = float(args['--vxSize'])
            except:
                exit("The voxel size (--vxSize) is not a valid floating point number.")

        if vxSize <= 0.0:
            print('vxSize:\t%.2f'       % vxSize)
            exit("The voxel size is not a positive number.")

        # --pVal
        try:
            pValue = float(args['--pVal'])
        except:
            exit("The confidence level (--pVal) is not a valid floating point number.")

        if pValue <= 0.0 or pValue > 0.05:
            exit("The confidence level (--pVal) is outside of the [0, 0.05] range.")

        # --minRes
        try:
            minRes = float(args['--minRes'])
        except:
            exit("The minimum resolution (--minRes) is not a valid floating point number.")

        if minRes < 0.0:
            exit("The minimum resolution (--minRes) is not a positive number.")

        # --maxRes
        try:
            maxRes = float(args['--maxRes'])
        except:
            exit("The maximum resolution (--maxRes) is not a valid floating point number.")

        if maxRes < 0.0:
            exit("The maximum resolution (--maxRes) is not a positive number.")

        # --stepRes
        try:
            stepRes = float(args['--stepRes'])
        except:
            exit("The step size (--stepRes) is not a valid floating point number.")

        if stepRes < 0.25:
            exit("The step size (--stepRes) is too small.")

        # --maskVol
        if args['--maskVol'] == None:
            dataMask = 0
        else:
            try:
                dataMask = MRC_Data(args['--maskVol'],'ccp4')
            except:
                exit("The mask volume (MRC/CCP4 format) could not be read.")

        # Call ResMap
        if args['--noguiSingle'] == True:
            ResMap_algorithm(
                    inputFileName    = inputFileName,
                    data             = data,
                    vxSize           = vxSize,
                    pValue           = pValue,
                    minRes           = minRes,
                    maxRes           = maxRes,
                    stepRes          = stepRes,
                    dataMask         = dataMask,
                    graphicalOutput  = args['--vis2D'],
                    chimeraLaunch    = args['--launchChimera'],
                    noiseDiagnostics = args['--noiseDiag']
                 )
        elif args['--noguiSplit'] == True:
            ResMap_algorithm(
                    inputFileName1   = inputFileName1,
                    inputFileName2   = inputFileName2,
                    data1            = data1,
                    data2            = data2,
                    vxSize           = vxSize,
                    pValue           = pValue,
                    minRes           = minRes,
                    maxRes           = maxRes,
                    stepRes          = stepRes,
                    dataMask         = dataMask,
                    graphicalOutput  = args['--vis2D'],
                    chimeraLaunch    = args['--launchChimera'],
                    noiseDiagnostics = args['--noiseDiag']
                 )
        else:
            print ("\n\nSomething somewhere went terribly wrong.\n\n")