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Merge branch 'develop_old'
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@mikesmic
mikesmic committed Mar 7, 2022
2 parents d8769c9 + c606f4b commit 4b49443
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14 changes: 14 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,20 @@
### Fixed


## 0.93.4 (07-03-2022)

### Changed
- Update BCC slip system file and add a separate FCC file with same ordering as in DAMASK
- Refactor boundary lines in `ebsd.map` class and add methods for warping lines to a DIC map
- Refactor `linkEbsdMap` method and pass all arguments to transform estimate method
- Remove IPython and jupyter as requirements
- Move slip systems to `Phase` class and load automatically based on crystal stucture
- Make Oxford bonary loader tolerate of unknown data fields

### Fixed
- Fix ebsd grain linker so it works again


## 0.93.3 (23-08-2021)

### Added
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5 changes: 5 additions & 0 deletions defdap/__init__.py
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Expand Up @@ -11,4 +11,9 @@
'find_grain_report_freq': 100,
# How to find grain in a HRDIC map, either 'floodfill' or 'warp'
'hrdic_grain_finding_method': 'floodfill',
'slip_system_file': {
'FCC': 'cubic_fcc',
'BCC': 'cubic_bcc',
'HCP': 'hexagonal_noca',
},
}
2 changes: 1 addition & 1 deletion defdap/_version.py
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@@ -1 +1 @@
__version__ = '0.93.3'
__version__ = '0.93.4'
199 changes: 111 additions & 88 deletions defdap/base.py
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Expand Up @@ -105,8 +105,8 @@ def plotGrainNumbers(self, dilateBoundaries=False, ax=None, **kwargs):
Set to true to dilate boundaries.
ax : matplotlib.axes.Axes, optional
axis to plot on, if not provided the current active axis is used.
kwargs : dict
Keyword arguments to pass to matplotlib.
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.plotting.MapPlot.addGrainNumbers`
Returns
-------
Expand All @@ -129,6 +129,8 @@ def locateGrainID(self, clickEvent=None, displaySelected=False, **kwargs):
Click handler to use.
displaySelected : bool, optional
If true, plot slip traces for grain selected by click.
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.base.Map.plotDefault`
"""
# Check that grains have been detected in the map
Expand Down Expand Up @@ -157,33 +159,41 @@ def clickGrainID(self, event, plot, displaySelected):
----------
event :
Click event.
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to capture clicks from.
displaySelected : bool
If true, plot the selected grain alone in pop-out window.
"""
if event.inaxes is plot.ax:
# grain id of selected grain
self.currGrainId = int(self.grains[int(event.ydata), int(event.xdata)] - 1)
print("Grain ID: {}".format(self.currGrainId))

# update the grain highlights layer in the plot
plot.addGrainHighlights([self.currGrainId], alpha=self.highlightAlpha)

if displaySelected:
currGrain = self[self.currGrainId]
if self.grainPlot is None or not self.grainPlot.exists:
self.grainPlot = currGrain.plotDefault(makeInteractive=True)
else:
self.grainPlot.clear()
self.grainPlot.callingGrain = currGrain
currGrain.plotDefault(plot=self.grainPlot)
self.grainPlot.draw()
# check if click was on the map
if event.inaxes is not plot.ax:
return

# grain id of selected grain
self.currGrainId = int(self.grains[int(event.ydata), int(event.xdata)] - 1)
print("Grain ID: {}".format(self.currGrainId))

# update the grain highlights layer in the plot
plot.addGrainHighlights([self.currGrainId], alpha=self.highlightAlpha)

if displaySelected:
currGrain = self[self.currGrainId]
if self.grainPlot is None or not self.grainPlot.exists:
self.grainPlot = currGrain.plotDefault(makeInteractive=True)
else:
self.grainPlot.clear()
self.grainPlot.callingGrain = currGrain
currGrain.plotDefault(plot=self.grainPlot)
self.grainPlot.draw()

def drawLineProfile(self, **kwargs):
"""Interactive plot for drawing a line profile of data.
Parameters
----------
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.base.Map.plotDefault`
"""
plot = self.plotDefault(makeInteractive=True, **kwargs)

Expand All @@ -198,21 +208,25 @@ def calcLineProfile(self, plot, startEnd, **kwargs):
Parameters
----------
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to calculate the line profile for.
startEnd : array_like
Selected points (x0, y0, x1, y1).
kwargs : dict, optional
Keyword arguments passed to :func:`matplotlib.pyplot.plot`
"""

x0, y0 = startEnd[0:2]
x1, y1 = startEnd[2:4]
profile_length = np.sqrt((y1 - y0) ** 2 + (x1 - x0) ** 2)

# Extract the values along the line
zi = profile_line(plot.imgLayers[0].get_array(),
(startEnd[1], startEnd[0]), (startEnd[3], startEnd[2]),
mode='nearest', **kwargs)
zi = profile_line(
plot.imgLayers[0].get_array(),
(startEnd[1], startEnd[0]),
(startEnd[3], startEnd[2]),
mode='nearest'
)
xi = np.linspace(0, profile_length, len(zi))

if self.profilePlot is None or not self.profilePlot.exists:
Expand All @@ -237,7 +251,7 @@ def setHomogPoint(self, binSize=1, points=None, **kwargs):
points : numpy.ndarray, optional
Array of (x,y) homologous points to set explicitly.
kwargs : dict, optional
Keyword arguments for matplotlib.
Keyword arguments passed to :func:`defdap.base.Map.plotHomog`
"""
if points is None:
Expand Down Expand Up @@ -269,17 +283,20 @@ def clickHomog(self, event, plot):
----------
event :
Click event.
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to monitor.
"""
if event.inaxes is plot.ax:
# right mouse click or shift + left mouse click
# shift click doesn't work in osx backend
if (event.button == 3 or
(event.button == 1 and event.key == 'shift')):
plot.addPoints([int(event.xdata)], [int(event.ydata)],
updateLayer=1)
# check if click was on the map
if event.inaxes is not plot.ax:
return

# right mouse click or shift + left mouse click
# shift click doesn't work in osx backend
if (event.button == 3 or
(event.button == 1 and event.key == 'shift')):
plot.addPoints([int(event.xdata)], [int(event.ydata)],
updateLayer=1)

def keyHomog(self, event, plot):
"""Event handler for moving position using keyboard after clicking on a map.
Expand All @@ -288,7 +305,7 @@ def keyHomog(self, event, plot):
----------
event :
Keypress event.
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to monitor.
"""
Expand Down Expand Up @@ -324,7 +341,7 @@ def clickSaveHomog(self, event, plot, binSize):
----------
event :
Button click event.
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to monitor.
binSize : int, optional
Binning applied to image, if applicable.
Expand Down Expand Up @@ -457,41 +474,43 @@ def clickGrainNeighbours(self, event, plot):
----------
event :
Click event.
plot : defdap.plotting.Plot
plot : defdap.plotting.MapPlot
Plot to monitor.
"""
if event.inaxes is plot.ax:
# grain id of selected grain
grainId = int(self.grains[int(event.ydata), int(event.xdata)] - 1)
if grainId < 0:
return
self.currGrainId = grainId
grain = self[grainId]
# check if click was on the map
if event.inaxes is not plot.ax:
return

# find first and second nearest neighbours
firstNeighbours = list(self.neighbourNetwork.neighbors(grain))
highlightGrains = [grain] + firstNeighbours

secondNeighbours = []
for firstNeighbour in firstNeighbours:
trialSecondNeighbours = list(
self.neighbourNetwork.neighbors(firstNeighbour)
)
for secondNeighbour in trialSecondNeighbours:
if (secondNeighbour not in highlightGrains and
secondNeighbour not in secondNeighbours):
secondNeighbours.append(secondNeighbour)
highlightGrains.extend(secondNeighbours)

highlightGrains = [grain.grainID for grain in highlightGrains]
highlightColours = ['white']
highlightColours.extend(['yellow'] * len(firstNeighbours))
highlightColours.append('green')

# update the grain highlights layer in the plot
plot.addGrainHighlights(highlightGrains,
grainColours=highlightColours)
# grain id of selected grain
grainId = int(self.grains[int(event.ydata), int(event.xdata)] - 1)
if grainId < 0:
return
self.currGrainId = grainId
grain = self[grainId]

# find first and second nearest neighbours
firstNeighbours = list(self.neighbourNetwork.neighbors(grain))
highlightGrains = [grain] + firstNeighbours

secondNeighbours = []
for firstNeighbour in firstNeighbours:
trialSecondNeighbours = list(
self.neighbourNetwork.neighbors(firstNeighbour)
)
for secondNeighbour in trialSecondNeighbours:
if (secondNeighbour not in highlightGrains and
secondNeighbour not in secondNeighbours):
secondNeighbours.append(secondNeighbour)
highlightGrains.extend(secondNeighbours)

highlightGrains = [grain.grainID for grain in highlightGrains]
highlightColours = ['white']
highlightColours.extend(['yellow'] * len(firstNeighbours))
highlightColours.append('green')

# update the grain highlights layer in the plot
plot.addGrainHighlights(highlightGrains, grainColours=highlightColours)

@property
def proxigram(self):
Expand Down Expand Up @@ -673,8 +692,8 @@ def plotGrainDataMap(
IDs of grains to plot for. Use -1 for all grains in the map.
bg: int or real, optional
Value to fill the background with.
kwargs:
Other parameters are passed to :func:`defdap.plotting.MapPlot.create`
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.plotting.MapPlot.create`
Returns
-------
Expand Down Expand Up @@ -710,18 +729,18 @@ def plotGrainDataIPF(
Parameters
----------
mapData : numpy.ndarray
Array of map data to grain average. This must be cropped!
direction : numpy.ndarray
Vector of reference direction for the IPF.
plotColourBar : bool, optional
Set to False to exclude the colour bar from the plot.
vmin : float, optional
Minimum value of colour scale.
vmax : float, optional
Maximum value for colour scale.
cLabel : str, optional
Colour bar label text.
mapData : numpy.ndarray
Array of map data. This must be cropped! Either mapData or
grainData must be supplied.
grainData : list or np.array, optional
Grain values. This an be a single value per grain or RGB
values. You must supply either mapData or grainData.
grainIds: list of int or int, optional
IDs of grains to plot for. Use -1 for all grains in the map.
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.quat.Quat.plotIPF`
"""
# Set default plot parameters then update with any input
Expand Down Expand Up @@ -759,6 +778,16 @@ def plotGrainDataIPF(
class Grain(object):
"""
Base class for a grain.
Attributes
----------
grainID : int
ownerMap : defdap.base.Map
coordList : list of tuples
"""
def __init__(self, grainID, ownerMap):
# list of coords stored as tuples (x, y). These are coords in a
Expand Down Expand Up @@ -861,7 +890,7 @@ def plotOutline(self, ax=None, plotScaleBar=False, **kwargs):
plotScaleBar : bool
plots the scale bar on the grain if true.
kwargs : dict
keyword arguments to pass to :func:`defdap.plotting.GrainPlot.addMap`.
keyword arguments passed to :func:`defdap.plotting.GrainPlot.addMap`
Returns
-------
Expand Down Expand Up @@ -1014,14 +1043,8 @@ def plotGrainData(self, mapData=None, grainData=None, **kwargs):
grainData : numpy.ndarray
List of data at each point in the grain. Either this or
'mapData' must be supplied and 'grainData' takes precedence.
vmin : float, optional
Minimum value of colour scale.
vmax : float, optional
Minimum value of colour scale.
cLabel : str, optional
Colour bar label text.
cmap : str, optional
Colour map to use, default is viridis.
kwargs : dict, optional
Keyword arguments passed to :func:`defdap.plotting.GrainPlot.create`
"""
# Set default plot parameters then update with any input
Expand Down
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