Reflection List

The ReflectionList class encapsulates a list of reflections; each reflection is defined by a unique reflection index , and contains an arbitrary amount of (floating point) properties. These properties are defined on the level of the reflection list; as such, a reflection list can be conceptualized as a table, where the rows contain the individual reflections, and the columns the properties.

Access to the entries in the reflection list is only possible by means of a reflection proxyter, which is obtained upon iterating over an existing list. The reflections are returned in a strict order, based on their index.

A reflection list contains a lattice and a unit cell. The former is usually in (fractional) pixel dimensions, referring to the image the reflections were originally extracted from. The latter represents the unit cell of the dataset. Neither of these two is mandatory, however, the conversion from reciprocal z values (the third component in the index) to fractional l stored in the mtz file during Export uses the thickness of the spatial unit cell!

Reflection lists can be saved to disk as mtz files, see the Reflection IO entry for more information.

Interface

Construction

ReflectionList()

Creates an empty reflection list with a default lattice and unit cell.

ReflectionList(Lattice lat)

Creates an empty reflection list with the given lattice and a default unit cell

ReflectionList(SpatialUnitCell uc)

Creates an empty reflection list with the given unit cell and a default lattice

ReflectionList(Lattice lat, SpatialUnitCell uc)

Creates an empty reflection list with the given lattice and unit cell

ReflectionList(SpatialUnitCell uc,Lattice lat)

see above

ReflectionList(ReflectionList& rl, bool full_copy=True)

Creates a new reflection list based on the given one; if the (optional) full_copy flag is False, only the skeleton will be copied, meaning the lattice, the unit cell, and the properties. The complete set of reflections will only be copied if the full_copy flag is True.

Properties

CopyProperties(ReflectionList rl)

Clears the list of reflections and all properties; it then creates a new set of properties from the given reflection list.

AddProperty(string prop, PropertyType type=PT_REAL)

Adds a new property by the name prop to the reflection list. All existing reflections will have a value of zero for this property. The second optional parameters allows a type to be assigned to the property, which mirrors the types as defined for the mtz format.

• PT_REAL
• PT_INDEX
• PT_INTENSITY
• PT_AMPLITUDE
• PT_ANOMALOUS_DIFFERENCE
• PT_STDDEV
• PT_AMPLITUDE2
• PT_STDDEVA2
• PT_INTENSITY2
• PT_STDDEVI2
• PT_NORM_AMPLITUDE
• PT_PHASE
• PT_WEIGHT
• PT_PHASE_PROB
• PT_BATCH
• PT_MISYM
• PT_INTEGER

bool HasPropertyType(PropertyType ptype)

Returns true if the reflection list has at least one property of the given type

string GetPropertyNameByType(PropertyType ptype)

Returns the name of the first property of the given type

bool HasProperty(string prop)

Returns true if the reflection list has a property of the given name

RenameProperty(string from, string& to)

Renames a property

SetPropertyType(string prop, PropertyType type)

Sets the property identified by its name to the given type

PropertyType GetPropertyType(string prop)

Returns the type of a property identified by its name

int GetPropertyCount()

Returns number of properties in reflection list

int GetPropertyIndex(string name)

Returns the internal index of the property identified by its name

string GetPropertyName(int n)

Returns the name of the property identified by its internal index

PropertyType GetPropertyType(int n)

Returns the type of the property identified by its internal index

stringlist GetPropertyList()

Returns all properties as a list of strings

Proxyters

Setters/Getters

Reflection Algorithms

Others

class iplt.ReflectionList((object)arg1)

AddBatch((ReflectionList)self, (int)batch_id, (Lattice)lattice) → None

AddProperty((ReflectionList)self, (str)prop[, (PropertyType)type=iplt._iplt_base.PropertyType.PT_REAL[, (float)default_value=0]]) → int

AddProxyter((ReflectionList)self, (ReflectionProxyter)rp) → ReflectionProxyter

AddReflection((ReflectionList)self, (ReflectionIndex)idx[, (int)batch_id=iplt._iplt_base.BATCH_ID.BATCH_ID_DEFAULT]) → ReflectionProxyter

AddReflection( (ReflectionList)self, (ReflectionIndex)idx, (ReflectionProxyter)rp) -> ReflectionProxyter

Apply((ReflectionList)self, (ReflectionNonModAlgorithm)alg) → None

Apply( (ReflectionList)self, (ReflectionModIPAlgorithm)alg) -> ReflectionList

Apply( (ReflectionList)self, (ReflectionConstModIPAlgorithm)alg) -> ReflectionList

Apply( (ReflectionList)self, (ReflectionModOPAlgorithm)alg) -> ReflectionList

Apply( (ReflectionList)self, (ReflectionConstModOPAlgorithm)alg) -> ReflectionList

ApplyIP((ReflectionList)self, (ReflectionNonModAlgorithm)alg) → None

ApplyIP( (ReflectionList)self, (ReflectionModIPAlgorithm)alg) -> None

ApplyIP( (ReflectionList)self, (ReflectionConstModIPAlgorithm)alg) -> None

ApplyIP( (ReflectionList)self, (ReflectionModOPAlgorithm)alg) -> None

ApplyIP( (ReflectionList)self, (ReflectionConstModOPAlgorithm)alg) -> None

Begin((ReflectionList)self) → ReflectionProxyter

ClearReflections((ReflectionList)self) → None

CopyProperties((ReflectionList)self, (ReflectionList)rlist) → None

CopyProxyter((ReflectionList)self, (ReflectionProxyter)rp) → ReflectionProxyter

DeleteProperty((ReflectionList)self, (str)prop) → None

Dump((ReflectionList)self) → str

DumpFormatted((ReflectionList)self) → str

DumpHeader((ReflectionList)self) → str

Find((ReflectionList)self, (ReflectionIndex)idx) → ReflectionProxyter

FindFirst((ReflectionList)self, (Point)hk) → ReflectionProxyter

GetBatchIds((ReflectionList)self) → IntList

GetLattice((ReflectionList)self[, (int)batch_id=iplt._iplt_base.BATCH_ID.BATCH_ID_DEFAULT]) → Lattice

GetNumBatches((ReflectionList)self) → int

GetPropertyCount((ReflectionList)self) → int

GetPropertyIndex((ReflectionList)self, (str)prop) → int

GetPropertyName((ReflectionList)self, (int)idx) → str

GetPropertyNameByType((ReflectionList)self, (PropertyType)type) → str

GetPropertyType((ReflectionList)self, (str)prop) → PropertyType

GetPropertyType( (ReflectionList)self, (int)idx) -> PropertyType

GetResolution((ReflectionList)self, (ReflectionIndex)idx) → float

GetSymmetry((ReflectionList)self) → Symmetry

GetUnitCell((ReflectionList)self) → SpatialUnitCell

HasProperty((ReflectionList)self, (str)prop) → bool

HasPropertyType((ReflectionList)self, (PropertyType)type) → bool

Merge((ReflectionList)self, (ReflectionList)rlist) → None

NumReflections((ReflectionList)self) → int

RemoveBatch((ReflectionList)self, (int)batch_id) → None

RenameProperty((ReflectionList)self, (str)from, (str)to) → None

SetActiveBatch((ReflectionList)self, (int)batch_id) → int

SetLattice((ReflectionList)self, (Lattice)lattice[, (int)batch_id=iplt._iplt_base.BATCH_ID.BATCH_ID_DEFAULT]) → None

SetPropertyType((ReflectionList)self, (str)prop, (PropertyType)type) → None

SetSymmetry((ReflectionList)self, (str)sym) → None

SetSymmetry( (ReflectionList)self, (Symmetry)sym) -> None

SetUnitCell((ReflectionList)self, (SpatialUnitCell)unitcell) → None

__init__((object)arg1) → None

__init__( (object)self, (ReflectionList)rlist [, (bool)copy=True]) -> None

__init__( (object)self, (int)batch_id, (Lattice)lattice) -> None

__init__( (object)self, (SpatialUnitCell)spatial_unitcell) -> None

__init__( (object)self, (SpatialUnitCell)spatial_unitcell, (int)batch_id, (Lattice)lattice) -> None

Examples

This code snippet creates the following reflection list:

index	amp	sigamp
(1,3,0.132)	23.45	4.54
(4,7,0.237)	17.33	6.13

import ex
# create new list and add two properties
rlist=ex.ReflectionList()
rlist.AddProperty("amp")
rlist.AddProperty("sigamp")

# add reflections by means of reflection proxyters
rp=rlist.AddReflection(ex.ReflectionList(2,3,0.132))
rp.Set("amp",23.45)
rp.Set("sigamp",4.54)
rp=rlist.AddReflection(ex.ReflectionList(4,7,0.237))
rp.Set("amp",17.33)
rp.Set("sigamp",6.13)

# iterate over list, again accessing the reflections via the proxyters
for rp in rlist:
  print rp.GetIndex(),rp.Get("amp"),rp.Get("sigamp")