def _defineParams(self, form):
""" Define the parameters that will be input for the Protocol.
This definition is also used to generate automatically the GUI.
"""
form.addSection(label='Input')
form.addParam(
'inputParticles',
PointerParam,
pointerClass='SetOfParticles',
pointerCondition='hasCTF',
label="Input particles with CTF",
help='Select the input particles. \n '
'they should have information about the CTF (hasCTF=True)')
form.addParam(
'ctfGroupMaxDiff',
FloatParam,
default=1,
label='Error for grouping',
validators=[GE(1., 'Error must be greater than 1')],
help='Maximum error when grouping, the higher the more groups'
'This is a 1D program, only defocus U is used\n '
'The frequency at which the phase difference between the CTFs\n'
'belonging to 2 particles is equal to Pi/2 is computed \n '
'If this difference is less than 1/(2*factor*sampling_rate)\n'
'then images are placed in different groups')
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputCoordinatesTiltedPairs',
PointerParam,
important=True,
label="Coordinates tilted pairs",
pointerClass='CoordinatesTiltPair',
help='Select the CoordinatesTiltPairs')
form.addParam('downsampleType',
EnumParam,
choices=['same as picking', 'other'],
default=0,
important=True,
label='Micrographs source',
display=EnumParam.DISPLAY_HLIST,
help='By default the particles will be extracted '
'from the micrographs used in the picking '
'step ( _same as picking_ option ).\n'
'If you select _other_ option, you must provide '
'a different set of micrographs to extract from.\n'
'*Note*: In the _other_ case, ensure that provided '
'micrographs and coordinates are related '
'by micName or by micId. Difference in pixel size '
'will be handled automatically.')
form.addParam('inputMicrographsTiltedPair',
PointerParam,
pointerClass='MicrographsTiltPair',
condition='downsampleType != 0',
important=True,
label='Input tilt pair micrographs',
help='Select the tilt pair micrographs from which to '
'extract.')
form.addParam(
'ctfUntilt',
PointerParam,
allowsNull=True,
# expertLevel=LEVEL_ADVANCED,
pointerClass='SetOfCTF',
label='CTF estimation (untilted mics)',
help='Choose some CTF estimation related to input '
'UNTILTED micrographs. \n CTF estimation is needed '
'if you want to do phase flipping or you want to '
'associate CTF information to the particles.')
form.addParam(
'ctfTilt',
PointerParam,
allowsNull=True,
# expertLevel=LEVEL_ADVANCED,
pointerClass='SetOfCTF',
label='CTF estimation (tilted mics)',
help='Choose some CTF estimation related to input '
'TILTED micrographs. \n CTF estimation is needed '
'if you want to do phase flipping or you want to '
'associate CTF information to the particles.')
# downFactor should always be 1.0 or greater
geOne = GE(1.0, error='Value should be greater or equal than 1.0')
form.addParam(
'downFactor',
FloatParam,
default=1.0,
validators=[geOne],
label='Downsampling factor',
help='Select a value greater than 1.0 to reduce the size '
'of micrographs before extracting the particles. '
'If 1.0 is used, no downsample is applied. '
'Non-integer downsample factors are possible. ')
form.addParam('boxSize',
IntParam,
default=0,
label='Particle box size',
validators=[Positive],
help='In pixels. The box size is the size of the boxed '
'particles, actual particles may be smaller than '
'this. If you do downsampling after extraction, '
'provide final box size here.')
form.addParam('doBorders',
BooleanParam,
default=False,
label='Fill pixels outside borders',
help='Xmipp by default skips particles whose boxes fall '
'outside of the micrograph borders. Set this '
'option to True if you want those pixels outside '
'the borders to be filled with the closest pixel '
'value available')
form.addSection(label='Preprocess')
form.addParam('doRemoveDust',
BooleanParam,
default=True,
important=True,
label='Dust removal (Recommended)',
help='Sets pixels with unusually large values to random '
'values from a Gaussian with zero-mean and '
'unity-standard deviation.')
form.addParam('thresholdDust',
FloatParam,
default=3.5,
condition='doRemoveDust',
expertLevel=LEVEL_ADVANCED,
label='Threshold for dust removal',
help='Pixels with a signal higher or lower than this '
'value times the standard deviation of the image '
'will be affected. For cryo, 3.5 is a good value. '
'For high-contrast negative stain, the signal '
'itself may be affected so that a higher value may '
'be preferable.')
form.addParam('doInvert',
BooleanParam,
default=None,
label='Invert contrast',
help='Invert the contrast if your particles are black '
'over a white background. Xmipp, Spider, Relion '
'and Eman require white particles over a black '
'background, Frealign (up to v9.07) requires black '
'particles over a white background')
form.addParam(
'doFlip',
BooleanParam,
default=False,
# expertLevel=LEVEL_ADVANCED,
label='Phase flipping',
help='Use the information from the CTF to compensate for '
'phase reversals.\n'
'Phase flip is recommended in Xmipp or Eman\n'
'(even Wiener filtering and bandpass filter are '
'recommended for obtaining better 2D classes)\n'
'Otherwise (Frealign, Relion, Spider, ...), '
'phase flip is not recommended.')
form.addParam('doNormalize',
BooleanParam,
default=True,
label='Normalize (Recommended)',
help='It subtract a ramp in the gray values and '
'normalizes so that in the background there is 0 '
'mean and standard deviation 1.')
form.addParam('normType',
EnumParam,
choices=['OldXmipp', 'NewXmipp', 'Ramp'],
default=2,
condition='doNormalize',
expertLevel=LEVEL_ADVANCED,
display=EnumParam.DISPLAY_COMBO,
label='Normalization type',
help='OldXmipp (mean(Image)=0, stddev(Image)=1).\n'
'NewXmipp (mean(background)=0, '
'stddev(background)=1)\n'
'Ramp (subtract background+NewXmipp).')
form.addParam('backRadius',
IntParam,
default=-1,
condition='doNormalize',
label='Background radius',
expertLevel=LEVEL_ADVANCED,
help='Pixels outside this circle are assumed to be '
'noise and their stddev is set to 1. Radius for '
'background circle definition (in pix.). If this '
'value is 0, then half the box size is used.')
form.addParallelSection(threads=4, mpi=1)
def _defineProjectionMatchingParams(self, form):
form.addSection(label='Input')
#SelFileName
form.addParam(
'inputParticles',
PointerParam,
label="Input particles",
important=True,
pointerClass='SetOfParticles',
help='Select the input particles. \n '
'If you want perform *CTF* correction the input particles \n '
'should have information about the CTF (hasCTF=True)')
form.addParam(
'useInitialAngles',
BooleanParam,
default=False,
label="Use initial angles/shifts ? ",
help=
'Set to *Yes* if you want to use the projection assignment (angles/shifts) \n '
'associated with the input particles (hasProjectionAssigment=True)')
# ReferenceFileNames
form.addParam('input3DReferences',
PointerParam,
pointerClass='Volume',
label='Initial 3D reference volume',
help='Input 3D reference reconstruction.')
form.addParam(
'cleanUpFiles',
BooleanParam,
default=False,
label="Clean up intermediate files?",
expertLevel=LEVEL_ADVANCED,
help='Save disc space by cleaning up intermediate files. \n '
'Be careful, many options of the visualization protocol will not work anymore, \n '
'since all class averages, selfiles etc will be deleted. ')
form.addSection(label='CTF correction & Mask')
groupCTF = form.addGroup('CTF correction')
groupCTF.addParam(
'doCTFCorrection',
BooleanParam,
default=True,
label="Perform CTF correction?",
help=
'If set to true, a CTF (amplitude and phase) corrected map will be refined, \n '
'and the data will be processed in CTF groups. \n\n '
'_NOTE_: You cannot combine CTF-correction with re-alignment of the classes. \n '
'Remember that CTF information should be provided in the images input file. \n '
)
groupCTF.addParam(
'doAutoCTFGroup',
BooleanParam,
default=True,
condition='doCTFCorrection',
label="Make CTF groups automatically?",
help=
'Make CTF groups based on a maximum differences at a given resolution limit. \n '
'_NOTE_: If this option is set to false, a docfile with the defocus values where to \n\n '
'split the images in distinct defocus group has to be provided (see expert option below) \n '
)
groupCTF.addParam(
'ctfGroupMaxDiff',
FloatParam,
default=0.1,
condition='doCTFCorrection and doAutoCTFGroup',
label='Maximum difference for grouping',
validators=[Positive],
help=
'If the difference between the CTF-values up to the resolution limit specified \n '
'below is larger than the value given here, two images will be placed in \n '
'distinct CTF groups.')
groupCTF.addParam(
'ctfGroupMaxResol',
FloatParam,
default=5.6,
condition='doCTFCorrection and doAutoCTFGroup',
label='Resolution limit (A) for grouping',
validators=[Positive],
help=
'Maximum resolution where to consider CTF-differences among different groups. \n '
'One should use somewhat higher resolutions than those aimed for in the refinement.'
)
# SplitDefocusDocFile
groupCTF.addParam(
'setOfDefocus',
StringParam,
label='Set of defocus',
default='',
condition='doCTFCorrection and not doAutoCTFGroup',
help='Set with defocus values where to split into groups. \n '
'This field is compulsory if you do not want to make the CTF groups automatically. \n\n '
'_NOTE_: The requested docfile can be made initially with the *xmipp_ctf_group* program, \n '
'and then it can be edited manually to suit your needs.')
groupCTF.addParam(
'paddingFactor',
FloatParam,
default=2,
condition='doCTFCorrection',
label='Padding factor',
validators=[GE(1)],
help=
'Application of CTFs to reference projections and of Wiener filter \n '
'to class averages will be done using padded images. \n '
'Use values larger than one to pad the images.')
groupCTF.addParam(
'wienerConstant',
FloatParam,
default=-1,
condition='doCTFCorrection',
label='Wiener constant',
expertLevel=LEVEL_ADVANCED,
help=
'Term that will be added to the denominator of the Wiener filter. \n '
'In theory, this value is the inverse of the signal-to-noise ratio \n '
'If a negative value is taken, the program will use a default value as in FREALIGN \n '
'(i.e. 10% of average sum terms over entire space) \n '
'see Grigorieff JSB 157 (2006) pp117-125')
#TODO: Use common mask parameters
groupMask = form.addGroup('Mask')
# doMask, doSphericalMask now merged into maskType
groupMask.addParam(
'maskType',
EnumParam,
choices=['None', 'circular', 'mask object'],
default=MASK2D_CIRCULAR,
label="Mask reference volumes",
display=EnumParam.DISPLAY_COMBO,
help=
'Masking the reference volume will increase the signal to noise ratio. \n '
'Do not provide a very tight mask. \n ')
groupMask.addParam(
'maskRadius',
IntParam,
default=-1,
condition='maskType == 1',
label='Radius of spherical mask (px)',
help='This is the radius (in pixels) of the spherical mask ')
groupMask.addParam(
'inputMask',
PointerParam,
pointerClass="VolumeMask",
allowNull=True,
label='Mask Object',
condition='maskType == 2',
help=
'The mask file should have the same dimensions as your input particles. \n '
'The protein region should be 1 and the solvent should be 0.')
# DataArePhaseFlipped , now taken from inputParticles.isPhaseFlipped()
# ReferenceIsCtfCorrected, now taken from input3DReferences.isAmplitudeCorrected()
form.addSection(label='Projection Matching')
form.addParam('numberOfIterations',
IntParam,
default=4,
label='Number of iterations',
help='Number of iterations to perform.')
form.addParam('innerRadius',
NumericListParam,
default='0',
label='Inner radius for rotational correlation:',
help=""" In pixels from the image center
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "8 8 2 2 "
specifies 4 iterations, the first two set the value to 8
and the last two to 2. An alternative compact notation
is ("2x8 2x0", i.e.,
2 iterations with value 8, and 2 with value 2).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam(
'outerRadius',
NumericListParam,
default='64',
label='Outer radius for rotational correlation',
help=
""" In pixels from the image center. Use a negative number to use the entire image.
*WARNING*: this radius will be use for masking before computing resolution
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "8 8 2 2 "
specifies 4 iterations, the first two set the value to 8
and the last two to 2. An alternative compact notation
is ("2x8 2x0", i.e.,
2 iterations with value 8, and 2 with value 2).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam(
'availableMemory',
IntParam,
default=2,
expertLevel=LEVEL_ADVANCED,
label='Available memory to store all references (Gb)',
help=
""" This is only for the storage of the references. If your projections do not fit in memory,
the projection matching program will run MUCH slower. But, keep in mind that probably
some additional memory is needed for the operating system etc.
Note that the memory per computing node needs to be given. That is, when using threads,
this value will be multiplied automatically by the number of (shared-memory) threads.
""")
form.addParam(
'angSamplingRateDeg',
NumericListParam,
default='7 5 3 2',
label='Angular sampling rate (deg)',
help=
""" Angular distance (in degrees) between neighboring projection points
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "8 8 2 2 "
specifies 4 iterations, the first two set the value to 8
and the last two to 2. An alternative compact notation
is ("2x8 2x0", i.e.,
2 iterations with value 8, and 2 with value 2).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('maxChangeInAngles',
NumericListParam,
default='1000 10 6 4',
label='Angular search range (deg)',
help=""" Maximum change in rot & tilt (in +/- degrees)
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1000 1000 10 10 "
specifies 4 iterations, the first two set the value to 1000 (no restriction)
and the last two to 10degrees. An alternative compact notation
is ("2x1000 2x10", i.e.,
2 iterations with value 1000, and 2 with value 10).
<Note:> if there are less values than iterations the last value is reused
<Note:> if there are more values than iterations the extra value are ignored
""")
form.addParam(
'perturbProjectionDirections',
NumericListParam,
default='0',
label='Perturb projection directions?',
expertLevel=LEVEL_ADVANCED,
help=
""" If set to 1, this option will result to a Gaussian perturbation to the
evenly sampled projection directions of the reference library.
This may serve to decrease the effects of model bias.
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1 1 0"
specifies 3 iterations, the first two set the value to 1
and the last to 0. An alternative compact notation
is ("2x1 0", i.e.,
2 iterations with value 1, and 1 with value 0).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
# Changed from String to Int
form.addParam(
'projectionMethod',
EnumParam,
choices=['fourier', 'real_space'],
default=PROJECT_REALSPACE,
expertLevel=LEVEL_ADVANCED,
label="Projection method",
display=EnumParam.DISPLAY_COMBO,
help=
'select projection method, by default Fourier with padding 1 and interpolation bspline'
)
form.addParam(
'paddingAngularProjection',
FloatParam,
default=1,
expertLevel=LEVEL_ADVANCED,
condition='projectionMethod == %d' % PROJECT_FOURIER,
label='Padding factor for projection',
validators=[GE(1)],
help="""Increase the padding factor will improve projection quality but
projection generation will be slower. In general padding 1 and spline is OK
""")
# Changed from String to Int
form.addParam(
'kernelAngularProjection',
EnumParam,
choices=['neareast', 'linear', 'bspline'],
default=KERNEL_BSPLINE,
expertLevel=LEVEL_ADVANCED,
condition='projectionMethod == %d' % PROJECT_FOURIER,
label='Interpolation kernel for projection',
help=""" Interpolation kernel for the generation of projections.
""")
form.addParam('maxChangeOffset',
NumericListParam,
default='1000 10 5',
label='Maximum change in origin offset',
expertLevel=LEVEL_ADVANCED,
help=""" Maximum shift allowed per iteration.
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1000 10 5"
specifies 3 iterations, the first two set the value to 1000
(almost no restriction) and the last to 5.
An alternative compact notation
is ("2x1000 5", i.e.,
2 iterations with value 1000, and 1 with value 5).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra values are ignored
""")
form.addParam(
'search5DShift',
NumericListParam,
default='4x5 0',
label='Search range for 5D translational search',
help=
""" Give search range from the image center for 5D searches (in +/- pixels).
Values larger than 0 will results in 5D searches (which may be CPU-intensive)
Give 0 for conventional 3D+2D searches.
Note that after the 5D search, for the optimal angles always
a 2D exhaustive search is performed anyway (making it ~5D+2D)
Provide a sequence of numbers (for instance, "5 5 3 0" specifies 4 iterations,
the first two set the value to 5, then one with 3, resp 0 pixels.
An alternative compact notation is ("3x5 2x3 0", i.e.,
3 iterations with value 5, and 2 with value 3 and the rest with 0).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam(
'search5DStep',
NumericListParam,
default='2',
label='Step size for 5D translational search',
expertLevel=LEVEL_ADVANCED,
help=
"""" Provide a sequence of numbers (for instance, "2 2 1 1" specifies 4 iterations,
the first two set the value to 2, then two with 1 pixel.
An alternative compact notation is ("2x2 2x1", i.e.,
2 iterations with value 2, and 2 with value 1).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('doRestricSearchbyTiltAngle',
BooleanParam,
default=False,
expertLevel=LEVEL_ADVANCED,
label="Restrict tilt angle search?",
help='Restrict tilt angle search \n ')
form.addParam('tilt0',
FloatParam,
default=0,
condition='doRestricSearchbyTiltAngle',
label="Lower-value for restricted tilt angle search",
help='Lower-value for restricted tilt angle search \n ')
form.addParam('tiltF',
FloatParam,
default=180,
condition='doRestricSearchbyTiltAngle',
label="Higher-value for restricted tilt angle search",
help='Higher-value for restricted tilt angle search \n ')
form.addParam(
'symmetry',
TextParam,
default='c1',
label='Point group symmetry',
help=" See %s for a description of the symmetry groups format."
"\nIf no symmetry is present, give c1. " % SYM_URL)
form.addParam('symmetryGroupNeighbourhood',
TextParam,
default='',
expertLevel=LEVEL_ADVANCED,
label='Symmetry group for Neighbourhood computations',
help=""" If you do not know what this is leave it blank.
This symmetry will be using for compute neighboring points,
but not for sampling or reconstruction
See [[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry][Symmetry]]
for a description of the symmetry groups format
If no symmetry is present, give c1
""")
form.addParam(
'onlyWinner',
NumericListParam,
default='0',
label='compute only closest neighbor',
expertLevel=LEVEL_ADVANCED,
condition="symmetryGroupNeighbourhood != ''",
help="""This option is only relevant if symmetryGroupNeighbourhood !=''
If set to 1 only one neighbor will be computed per sampling point
You may specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1 1 0"
specifies 3 iterations, the first two set the value to 1
and the last to 0. An alternative compact notation
is ("2x1 0", i.e.,
2 iterations with value 1, and 1 with value 0).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('discardImages',
EnumParam,
choices=['None', 'maxCC', 'percentage', 'classPercentage'],
default=SELECT_NONE,
display=EnumParam.DISPLAY_COMBO,
label='Discard images?',
help="""
None : No images will be discarded.
maxCC : Minimum Cross Correlation, discard images with CC below a fixed value.
percentage : Discard percentage of images with less CC.
classPercentage: Discard percentage of images in each projection direction with less CC.
Value of each option is set below.
""")
form.addParam('minimumCrossCorrelation',
NumericListParam,
default='0.1',
label='discard image if CC below',
condition='discardImages==%d' % SELECT_MAXCC,
help="""
Discard images with cross-correlation (CC) below this value.
Provide a sequence of numbers (for instance, "0.3 0.3 0.5 0.5" specifies 4 iterations,
the first two set the value to 0.3, then two with 0.5.
An alternative compact notation would be ("2x0.3 2x0.5").
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('discardPercentage',
NumericListParam,
default='10',
label='discard image percentage with less CC',
condition='discardImages==%d' % SELECT_PERCENTAGE,
help="""
Discard this percentage of images with less cross-correlation (CC)
Provide a sequence of numbers (for instance, "20 20 10 10" specifies 4 iterations,
the first two set the value to 20%, then two with 10%
An alternative compact notation would be ("2x20 2x10").
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
Set to zero to prevent discarding any images
""")
form.addParam('discardPercentagePerClass',
NumericListParam,
default='10',
label='discard image percentage in class with less CC',
condition='discardImages==%d' % SELECT_CLASSPERCENTAGE,
help="""
Discard this percentage of images in each class(projection direction)
with less cross-correlation (CC)
Provide a sequence of numbers (for instance, "20 20 10 10" specifies 4 iterations,
the first two set the value to 20%, then two with 10%
An alternative compact notation would be ("2x20 2x10").
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
Set to zero to prevent discarding any images
""")
form.addParam(
'doScale',
BooleanParam,
default=False,
label="Perform scale search?",
expertLevel=LEVEL_ADVANCED,
help=' If true perform scale refinement. (UNDER DEVELOPMENT!!!!) \n ')
form.addParam(
'scaleStep',
NumericListParam,
default=1,
condition='doScale',
label='Step scale factors size',
help='''Scale step factor size (1 means 0.01 in/de-crements around 1).
Provide a sequence of numbers (for instance, "1 1 .5 .5" specifies 4 iterations,
the first two set the value to 1%, then two with .5%
An alternative compact notation would be ("2x1 2x0.5").
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
Set to zero to prevent discarding any images''')
form.addParam('scaleNumberOfSteps',
NumericListParam,
default=3,
condition='doScale',
label='Number of scale steps',
help="""
Number of scale steps.
With default values (ScaleStep='1' and ScaleNumberOfSteps='3'): 1 +/-0.01 | +/-0.02 | +/-0.03.
With values ScaleStep='2' and ScaleNumberOfSteps='4' it performs a scale search over:
1 +/-0.02 | +/-0.04 | +/-0.06 | +/-0.08.
In general scale correction should only be applied to the last iteration. Do not use it unless
your data is fairly well aligned.
""")
form.addParam('projMatchingExtra',
StringParam,
default='',
label='Additional options for Projection_Matching',
expertLevel=LEVEL_ADVANCED,
help=""" For details see:
[[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Projection_matching][projection matching]] and
[[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Mpi_projection_matching][mpi projection matching]]
try -Ri xx -Ro yy for restricting angular search (xx and yy are
the particle inner and outter radius)
""")
#DoSaveImagesAssignedToClasses you can get this information in visualize
form.addSection(label='2D re-alignment of classes',
expertLevel=LEVEL_ADVANCED)
form.addParam('performAlign2D',
BooleanParam,
default=False,
label='Perform 2D re-alignment')
form.addParam(
'doAlign2D',
NumericListParam,
default='0',
condition='performAlign2D',
label='Perform 2D re-alignment of classes?',
help=""" After performing a 3D projection matching iteration, each of the
subsets of images assigned to one of the library projections is
re-aligned using a 2D-alignment protocol.
This may serve to remove model bias.
For details see:
[[http://xmipp.cnb.uam.es/twiki/bin/view/Xmipp/Align2d][align 2d]]
Note that you cannot combine this option with CTF-correction!
You may specify this option for each iteration.
This can be done by a sequence of 0 or 1 numbers (for instance, "1 1 0 0"
specifies 4 iterations, the first two applied alig2d while the last 2
dont. An alternative compact notation is
is ("2x1 2x0", i.e.,
2 iterations with value 1, and 2 with value 0).
*Note:*if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
*IMPORTANT:* if you set this variable to 0 the output of the projection
muching step will be copied as output of align2d
""")
form.addParam('align2DIterNr',
NumericListParam,
default='4',
condition='performAlign2D',
label='Number of align2d iterations:',
expertLevel=LEVEL_ADVANCED,
help=""" Use at least 3 iterations
The number of align iteration may change in each projection matching iteration
Ffor instance, "4 4 3 3 "
specifies 4 alig2d iterations in the first projection matching iteration
and two 3 alig2d iteration in the last 2 projection matching iterations.
An alternative compact notation
is ("2x4 2x3", i.e.,
2 iterations with value 4, and 2 with value 3).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('align2dMaxChangeOffset',
NumericListParam,
default='2x1000 2x10',
condition='performAlign2D',
label='Maximum change in origin offset (+/- pixels)',
expertLevel=LEVEL_ADVANCED,
help="""Maximum change in shift (+/- pixels)
You must specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1000 1000 10 10 "
specifies 4 iterations, the first two set the value to 1000 (no restriction)
and the last two to 10degrees. An alternative compact notation
is ("2x1000 2x10", i.e.,
2 iterations with value 1000, and 2 with value 10).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('align2dMaxChangeRot',
NumericListParam,
default='2x1000 2x20',
condition='performAlign2D',
label='Maximum change in rotation (+/- degrees)',
expertLevel=LEVEL_ADVANCED,
help="""Maximum change in shift (+/- pixels)
You must specify this option for each iteration.
This can be done by a sequence of numbers (for instance, "1000 1000 10 10 "
specifies 4 iterations, the first two set the value to 1000 (no restriction)
and the last two to 10degrees. An alternative compact notation
is ("2x1000 2x10", i.e.,
2 iterations with value 1000, and 2 with value 10).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addSection(label='3D Reconstruction')
form.addParam('reconstructionMethod',
EnumParam,
expertLevel=LEVEL_ADVANCED,
choices=['fourier', 'art', 'wbp'],
default=RECONSTRUCT_FOURIER,
display=EnumParam.DISPLAY_COMBO,
label='Reconstruction method',
help=""" Select what reconstruction method to use.
fourier: Fourier space interpolation (with griding).
art: Agebraic reconstruction technique
wbp : Weight back project method.
""")
form.addParam('fourierMaxFrequencyOfInterest',
DigFreqParam,
default=0.25,
condition='reconstructionMethod == %d' % RECONSTRUCT_FOURIER,
label='Initial maximum frequency',
expertLevel=LEVEL_ADVANCED,
help=""" This number is only used in the first iteration.
From then on, it will be set to resolution computed in the resolution section
""")
form.addParam('fourierReconstructionExtraCommand',
StringParam,
default='',
condition='reconstructionMethod == %d' % RECONSTRUCT_FOURIER,
label='Additional parameters for fourier',
expertLevel=LEVEL_ADVANCED,
help=""" For details see:
[[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Fourier][fourier]]
""")
form.addParam(
'artLambda',
NumericListParam,
default='0.2',
condition='reconstructionMethod == %d' % RECONSTRUCT_ART,
label='Values of lambda for ART',
expertLevel=LEVEL_ADVANCED,
help=
""" *IMPORTANT:* ou must specify a value of lambda for each iteration even
if ART has not been selected.
*IMPORTANT:* NOte that we are using the WLS version of ART that
uses geater lambdas than the plain art.
See for details:
[[http://xmipp.cnb.uam.es/twiki/bin/view/Xmipp/Art][xmipp art]]
You must specify this option for each iteration.
This can be done by a sequence of numbers (for instance, ".1 .1 .3 .3"
specifies 4 iterations, the first two set the value to 0.1
(no restriction)
and the last two to .3. An alternative compact notation
is ("2x.1 2x.3").
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('artReconstructionExtraCommand',
StringParam,
default='-k 0.5 -n 10 ',
condition='reconstructionMethod == %d' % RECONSTRUCT_ART,
label='Additional parameters for ART',
expertLevel=LEVEL_ADVANCED,
help=""" For details see:
[[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Art][xmipp art]]
""")
form.addParam('wbpReconstructionExtraCommand',
StringParam,
default='',
condition='reconstructionMethod == %d' % RECONSTRUCT_WBP,
label='Additional parameters for WBP',
expertLevel=LEVEL_ADVANCED,
help=""" For details see:
[[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Wbp][xmipp wbp]]
""")
form.addParam('doComputeResolution',
BooleanParam,
default=True,
label='Compute resolution?',
expertLevel=LEVEL_ADVANCED,
help=""" For details see:
[[http://xmipp.cnb.uam.es/twiki/bin/view/Xmipp/Resolution][xmipp resolution]].
""")
form.addParam('doSplitReferenceImages',
NumericListParam,
default='1',
label='Split references averages?',
expertLevel=LEVEL_ADVANCED,
condition="doComputeResolution",
help="""In theory each reference average should be splited
in two when computing the resolution. In this way each
projection direction will be represented in each of the
subvolumes used to compute the resolution. A much faster
but less accurate approach is to split the
proyection directions in two but not the averages. We
recommend the first approach for small volumes and the second for
large volumes (especially when using small angular
sampling rates.
*IMPORTANT:* the second option has ONLY been implemented for FOURIER
reconstruction method. Other reconstruction methods require this
flag to be set to True
You may specify this option for each iteration.
This can be done by a sequence of 0 or 1 numbers (for instance, "1 1 0 0"
specifies 4 iterations, the first two split the images while the last 2
don't. an alternative compact notation is
is ("2x1 2x0", i.e.,
2 iterations with value 1, and 2 with value 0).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more vapplications/scripts/protocols/new_protocol_projmatch.pyalues than iterations the extra value are ignored
""")
form.addParam('doLowPassFilter',
BooleanParam,
default=True,
label="Low-pass filter the reference?")
form.addParam(
'useFscForFilter',
BooleanParam,
default=True,
label='Use estimated resolution for low-pass filtering?',
condition="doLowPassFilter",
help=
""" If set to true, the volume will be filtered at a frecuency equal to
the resolution computed with a FSC=0.5 threshold, possibly
plus a constant provided by the user in the next input box.
If set to false, then the filtration will be made at the constant
value provided by the user in the next box (in digital frequency,
i.e. pixel^-1: minimum 0, maximum 0.5)
""")
form.addParam(
'constantToAddToFiltration',
NumericListParam,
default='0.05',
label='Constant to be added to the estimated resolution',
condition="doLowPassFilter",
help=""" The meaning of this field depends on the previous flag.
If set to true, then the volume will be filtered at a frequency equal to
the resolution computed with resolution_fsc (FSC=0.5) plus the value
provided in this field
If set to false, the volume will be filtered at the resolution
provided in this field
This value is in digital frequency, or pixel^-1: minimum 0, maximum 0.5
If you detect correlation between noisy regions decrease this value
(even to negative values)
You can specify this option for each iteration.
This can be done by a sequence of numbers (for instance, ".15 .15 .1 .1"
specifies 4 iterations, the first two set the constant to .15
and the last two to 0.1. An alternative compact notation
is ("2x.15 2x0.1", i.e.,
4 iterations with value 0.15, and three with value .1).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam(
'constantToAddToMaxReconstructionFrequency',
NumericListParam,
default='0.1',
label='Constant to be added to the reconstruction maximum frequency',
expertLevel=LEVEL_ADVANCED,
condition="doLowPassFilter",
help=
""" The meaning of this field depends on the <use FSC for filter> flag.
If set to true, then the volume will be reconstructed up to the frequency equal to
the resolution computed with resolution_fsc (FSC=0.5) plus the value
provided in this field
If set to false, the volume will be reconstructed up to the resolution
provided in this field
This value is in digital frequency, or pixel^-1: minimum 0, maximum 0.5
You can specify this option for each iteration.
This can be done by a sequence of numbers (for instance, ".15 .15 .1 .1"
specifies 4 iterations, the first two set the constant to .15
and the last two to 0.1. An alternative compact notation
is ("2x.15 2x0.1", i.e.,
4 iterations with value 0.15, and three with value .1).
*Note:* if there are less values than iterations the last value is reused
*Note:* if there are more values than iterations the extra value are ignored
""")
form.addParam('mpiJobSize',
IntParam,
default=2,
label='MPI job size',
expertLevel=LEVEL_ADVANCED,
help="""Minimum size of jobs in mpi processes.
Set to 1 for large images (e.g. 500x500)
and to 10 for small images (e.g. 100x100)
""")
form.addParallelSection(threads=1, mpi=8)