From f96733102869aa6a27eb2949f53b7177be5f363f Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Tue, 12 Apr 2022 10:07:10 +0200
Subject: [PATCH] Preview as float32 without nan, improved scenes
---
src/calng/DetectorAssembler.py | 28 +++++--
src/calng/scenes.py | 135 ++++++++++++++++++++++++---------
2 files changed, 123 insertions(+), 40 deletions(-)
diff --git a/src/calng/DetectorAssembler.py b/src/calng/DetectorAssembler.py
index 56178d94..dbfd2222 100644
--- a/src/calng/DetectorAssembler.py
+++ b/src/calng/DetectorAssembler.py
@@ -5,6 +5,7 @@ import re
import numpy as np
from karabo.bound import (
DOUBLE_ELEMENT,
+ FLOAT_ELEMENT,
IMAGEDATA_ELEMENT,
NDARRAY_ELEMENT,
NODE_ELEMENT,
@@ -131,6 +132,20 @@ class DetectorAssembler(TrainMatcher.TrainMatcher):
.reconfigurable()
.commit(),
+ FLOAT_ELEMENT(expected)
+ .key("preview.replaceNanWith")
+ .description(
+ "Displaying images in KaraboGUI seems to not go well when there are "
+ "NaN values in data. And there will be with bad pixel masking or just "
+ "geometry space between modules. NaN values get replaced with this "
+ "value to get around this; choose a value which clearly stands out "
+ "from the image data you want to see."
+ )
+ .assignmentOptional()
+ .defaultValue(-1000)
+ .reconfigurable()
+ .commit(),
+
DOUBLE_ELEMENT(expected)
.key("preview.maxRate")
.displayedName("Max rate")
@@ -241,7 +256,9 @@ class DetectorAssembler(TrainMatcher.TrainMatcher):
return
self._geometry = geom_utils.deserialize_geometry(serialized_geometry)
# TODO: allow multiple memory cells (extra geom notion of extra dimensions)
- self._stack_input_buffer = np.zeros(self._geometry.expected_data_shape)
+ self._stack_input_buffer = np.zeros(
+ self._geometry.expected_data_shape, dtype=np.float32
+ )
def on_matched_data(self, train_id, sources):
if self._geometry is None:
@@ -265,9 +282,9 @@ class DetectorAssembler(TrainMatcher.TrainMatcher):
# prepare for assembly
# TODO: handle failure to "parse" source, get data out
module_index = self._source_to_index(source)
- self._stack_input_buffer[module_index] = np.squeeze(
- data.get(self._path_to_stack)
- )
+ self._stack_input_buffer[module_index] = data.get(
+ self._path_to_stack
+ ).astype(np.float32, copy=False) # TODO: set dtype based on input?
module_indices_unfilled.discard(module_index)
earliest_source_timestamp = min(
earliest_source_timestamp, source_timestamp.toTimestamp()
@@ -308,11 +325,12 @@ class DetectorAssembler(TrainMatcher.TrainMatcher):
np, self.unsafe_get("preview.downsamplingFunction")
),
)
+ assembled[np.isnan(assembled)] = self.unsafe_get("preview.replaceNanWith")
output_hash = Hash(
"image.data",
ImageData(
# TODO: get around this being mirrored...
- assembled.astype(np.int32)[::-1, ::-1],
+ assembled[::-1, ::-1],
Dims(*assembled.shape),
Encoding.GRAY,
bitsPerPixel=32,
diff --git a/src/calng/scenes.py b/src/calng/scenes.py
index ed9dd89e..68bfa38a 100644
--- a/src/calng/scenes.py
+++ b/src/calng/scenes.py
@@ -17,6 +17,7 @@ from karabo.common.scenemodel.api import (
IntLineEditModel,
LabelModel,
LineEditModel,
+ LineModel,
RectangleModel,
SceneModel,
SceneTargetWindow,
@@ -138,6 +139,23 @@ class Space:
return []
+class Hline:
+ def __init__(self, width):
+ self.width = width
+ self.height = 0
+
+ def render(self, x, y):
+ return [
+ LineModel(
+ stroke="#000000",
+ x1=x,
+ x2=x+self.width,
+ y1=y,
+ y2=y,
+ )
+ ]
+
+
def dummy_wrap(model_class):
class Wrapper:
def __init__(self, *args, **kwargs):
@@ -557,6 +575,16 @@ class AssemblerDeviceStatus(VerticalLayout):
width=7 * BASE_INC,
height=BASE_INC,
)
+ rate = DisplayRoundedFloat(
+ keys=[f"{device_id}.outProcessing"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ )
+ tof = DisplayRoundedFloat(
+ keys=[f"{device_id}.timeOfFlight"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ )
self.children.extend(
[
name,
@@ -565,37 +593,9 @@ class AssemblerDeviceStatus(VerticalLayout):
train_id,
padding=0,
),
- LabelModel(
- text="Image downsampling",
- width=14 * BASE_INC,
- height=BASE_INC,
- ),
- HorizontalLayout(
- LabelModel(
- text="Factor",
- width=7 * BASE_INC,
- height=BASE_INC,
- ),
- ComboBoxModel(
- keys=[f"{device_id}.preview.downsamplingFactor"],
- width=7 * BASE_INC,
- height=BASE_INC,
- klass="EditableComboBox",
- ),
- padding=0,
- ),
HorizontalLayout(
- LabelModel(
- text="Function",
- width=7 * BASE_INC,
- height=BASE_INC,
- ),
- ComboBoxModel(
- keys=[f"{device_id}.preview.downsamplingFunction"],
- width=7 * BASE_INC,
- height=BASE_INC,
- klass="EditableComboBox",
- ),
+ rate,
+ tof,
padding=0,
),
DeviceSceneLinkModel(
@@ -606,6 +606,16 @@ class AssemblerDeviceStatus(VerticalLayout):
width=14 * BASE_INC,
height=BASE_INC,
),
+ LabelModel(
+ text="My geometry device:",
+ width=14 * BASE_INC,
+ height=BASE_INC,
+ ),
+ DisplayLabelModel(
+ keys=[f"{device_id}.geometryDevice"],
+ width=14 * BASE_INC,
+ height=BASE_INC,
+ ), # TODO: some day, get dynamic link to this friend
]
)
@@ -1131,12 +1141,67 @@ def detector_assembler_overview(device_id):
return VerticalLayout(
HorizontalLayout(
AssemblerDeviceStatus(device_id),
- titled("My geometry device")(boxed(VerticalLayout))(
- DisplayLabelModel(
- keys=[f"{device_id}.geometryDevice"],
- width=6 * BASE_INC,
+ titled("Preview settings")(boxed(VerticalLayout))(
+ HorizontalLayout(
+ LabelModel(
+ text="Display NaN values as:",
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ DoubleLineEditModel(
+ keys=[f"{device_id}.preview.replaceNanWith"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ padding=0,
+ ),
+ HorizontalLayout(
+ LabelModel(
+ text="Max preview rate",
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ DoubleLineEditModel(
+ keys=[f"{device_id}.preview.maxRate"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ padding=0,
+ ),
+ Hline(width=14 * BASE_INC),
+ LabelModel(
+ text="Image downsampling",
+ width=14 * BASE_INC,
height=BASE_INC,
- )
+ ),
+ HorizontalLayout(
+ LabelModel(
+ text="Factor",
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ ComboBoxModel(
+ keys=[f"{device_id}.preview.downsamplingFactor"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ klass="EditableComboBox",
+ ),
+ padding=0,
+ ),
+ HorizontalLayout(
+ LabelModel(
+ text="Function",
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ ),
+ ComboBoxModel(
+ keys=[f"{device_id}.preview.downsamplingFunction"],
+ width=7 * BASE_INC,
+ height=BASE_INC,
+ klass="EditableComboBox",
+ ),
+ padding=0,
+ ),
),
),
titled("Preview image")(boxed(dummy_wrap(DetectorGraphModel)))(
--
GitLab