diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 7290f54f7a079c69360b7542e7be517015e6e955..c492e7a8d8f74c6ce46216c8f2cff7b8fbc78d5d 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -28,7 +28,7 @@ from cal_tools.agipdutils import (
melt_snowy_pixels,
)
from cal_tools.enums import AgipdGainMode, BadPixels, SnowResolution
-from cal_tools.litpx_counter import AnalysisAddon, LitPixelCounter
+from cal_tools.litpx_counter import LitPixelCounter
from logging import warning
@@ -73,7 +73,7 @@ class AgipdCtrl:
else:
raise ValueError(f"No raw images found for {self.image_src}")
- return ncell
+ return ncell
def get_num_cells(self) -> int:
"""Read number of memory cells from fast data."""
@@ -84,7 +84,7 @@ class AgipdCtrl:
# the function returns wrong value.
ncell = self._get_num_cells_instr()
- return ncell
+ return ncell
def _get_acq_rate_ctrl(self) -> Optional[float]:
"""Get acquisition (repetition) rate from CONTROL source."""
@@ -588,6 +588,7 @@ class AgipdCorrections:
# Output parameters
self.compress_fields = ['gain', 'mask']
self.recast_image_fields = {}
+ self.write_extra_data = []
# Shared variables for data and constants
self.shared_dict = []
@@ -777,12 +778,13 @@ class AgipdCorrections:
instrument_channels.append(f"{agipd_base}/image")
# backward compatibility END
- addons = []
- for name, elem in data_dict.items():
- if isinstance(elem, AnalysisAddon):
- src_name = elem.source_name(karabo_id, det_channel)
- addons.append((elem, src_name))
- instrument_channels.append(f"{src_name}/{elem.channel}")
+ # resolve names for extra source
+ extra_sources = []
+ for name in self.write_extra_data:
+ processor = data_dict[name]
+ src_name = processor.source_name(karabo_id, det_channel)
+ extra_sources.append((processor, src_name))
+ instrument_channels.append(f"{src_name}/{processor.channel}")
with DataFile.from_details(out_folder, agg, runno, seqno) as outfile:
outfile.create_metadata(
@@ -823,13 +825,13 @@ class AgipdCorrections:
field, shape=arr.shape, dtype=arr.dtype, **kw
)
- # create addon sources
- required_addon_data = []
- for addon, src_name in addons:
+ # create extra sources
+ required_data = []
+ for processor, src_name in extra_sources:
src = outfile.create_instrument_source(src_name)
- addon.set_num_images(n_img)
- addon.create_schema(src, trains, count)
- required_addon_data.append((addon, src))
+ processor.set_num_images(n_img)
+ processor.create_schema(src, trains, count)
+ required_data.append((processor, src))
# Write the corrected data
for field in image_fields:
@@ -840,9 +842,9 @@ class AgipdCorrections:
else:
image_grp[field][:] = data_dict[field][:n_img]
- # write addon data
- for addon, src in required_addon_data:
- addon.write(src)
+ # write extra data
+ for processor, src in required_data:
+ processor.write(src)
def _write_compressed_frames(self, dataset, arr):
"""Compress gain/mask frames in multiple threads, and save their data
@@ -1493,6 +1495,7 @@ class AgipdCorrections:
:param shape: Shape of expected data (nImg, x, y)
:param n_cores_files: Number of files, handled in parallel
"""
+ self.write_extra_data = []
self.shared_dict = []
for i in range(n_cores_files):
self.shared_dict.append({})
@@ -1521,6 +1524,9 @@ class AgipdCorrections:
self.shared_dict[i]["litpx_counter"] = LitPixelCounter(
self.shared_dict[i], threshold=self.litpx_threshold)
+ if self.corr_bools.get("count_lit_pixels"):
+ self.write_extra_data.append("litpx_counter")
+
if self.corr_bools.get("round_photons"):
self.shared_hist_preround = sharedmem.empty(len(self.hist_bins_preround) - 1, dtype="i8")
self.shared_hist_postround = sharedmem.empty(len(self.hist_bins_postround) - 1, dtype="i8")
diff --git a/src/cal_tools/litpx_counter.py b/src/cal_tools/litpx_counter.py
index aec381bf0b3d8fdcb1e536b4df5b426c9cc4f21c..680292444f9d830b5e6abf98305fda21aaf1948b 100644
--- a/src/cal_tools/litpx_counter.py
+++ b/src/cal_tools/litpx_counter.py
@@ -2,16 +2,30 @@ import numpy as np
import sharedmem
-class AnalysisAddon:
- """Base class for analysis addons"""
+class LitPixelCounter:
+ """Lit-pixel counter: counts pixels with a signal above a threshold."""
- channel = "data"
+ channel = "litpx"
output_fields = [
- "cellId", "pulseId", "trainId"]
+ "cellId", "pulseId", "trainId",
+ "litPixels", "unmaskedPixels", "totalIntensity"
+ ]
required_data = [
- "cellId", "pulseId", "trainId"]
+ "data", "mask", "cellId", "pulseId", "trainId"
+ ]
- def __init__(self, data):
+ def __init__(self, data, threshold=0.7):
+ """Initialize the instance of lit-pixel analysis addon.
+
+ Parameters
+ ----------
+ data: dict
+ Dictionary with image data. It must include the fields:
+ `data`, `mask`, `cellId`, `pulseId`, `trainId`
+ threshold: float
+ The pixel intensity value, which if exceeded means
+ that the pixel is illuminated.
+ """
required_data = set(self.required_data) | {"pulseId"}
for name in required_data:
if name not in data:
@@ -21,6 +35,19 @@ class AnalysisAddon:
self.max_images = data["pulseId"].shape[0]
self.num_images = self.max_images
+ # specific members
+ self.image = data["data"]
+ self.mask = data["mask"]
+
+ self.threshold = threshold
+ self.num_unmasked_px = sharedmem.full(self.max_images, 0, int)
+ self.num_lit_px = sharedmem.full(self.max_images, 0, int)
+ self.total_intensity = sharedmem.full(self.max_images, 0, int)
+
+ self.data["litPixels"] = self.num_lit_px
+ self.data["unmaskedPixels"] = self.num_unmasked_px
+ self.data["totalIntensity"] = self.total_intensity
+
def set_num_images(self, num_images):
"""Sets the actual number of images in data.
@@ -39,7 +66,14 @@ class AnalysisAddon:
chunk: slice, sequence or array
The indices of images in `data` to process
"""
- raise NotImplementedError
+ ix = range(*chunk.indices(self.num_images))
+ for i in ix:
+ mask = self.mask[i] == 0
+ self.total_intensity[i] = np.sum(
+ self.image[i], initial=0, where=mask)
+ self.num_lit_px[i] = np.sum(
+ self.image[i] > self.threshold, initial=0, where=mask)
+ self.num_unmasked_px[i] = np.sum(mask)
def source_name(self, karabo_id, channel):
"""Returns the source name.
@@ -56,7 +90,7 @@ class AnalysisAddon:
source_name: str
The source name for EXDF files
"""
- return f"{karabo_id}/DANA/{channel}"
+ return f"{karabo_id}/LITPX/{channel}"
def create_schema(self, source, file_trains=None, count=None):
"""Creates the indices and keys in the source.
@@ -106,55 +140,3 @@ class AnalysisAddon:
channel = source[self.channel]
for key in self.output_fields:
channel[key][:] = self.data[key][:self.num_images]
-
-
-class LitPixelCounter(AnalysisAddon):
- """Lit-pixel counter analysis addon."""
-
- channel = "litpx"
- output_fields = [
- "cellId", "pulseId", "trainId",
- "litPixels", "unmaskedPixels", "totalIntensity"
- ]
- required_data = [
- "data", "mask", "cellId", "pulseId", "trainId"
- ]
-
- def __init__(self, data, threshold=0.8):
- """Initialize the instance of lit-pixel analysis addon.
-
- Parameters
- ----------
- data: dict
- Dictionary with image data. It must include the fields:
- `data`, `mask`, `cellId`, `pulseId`, `trainId`
- threshold: float
- The pixel intensity value, which if exceeded means
- that the pixel is illuminated.
- """
- super().__init__(data)
-
- self.image = data["data"]
- self.mask = data["mask"]
-
- self.threshold = threshold
- self.num_unmasked_px = sharedmem.full(self.max_images, 0, int)
- self.num_lit_px = sharedmem.full(self.max_images, 0, int)
- self.total_intensity = sharedmem.full(self.max_images, 0, int)
-
- self.data["litPixels"] = self.num_lit_px
- self.data["unmaskedPixels"] = self.num_unmasked_px
- self.data["totalIntensity"] = self.total_intensity
-
- def process(self, chunk):
- ix = range(*chunk.indices(self.num_images))
- for i in ix:
- mask = self.mask[i] == 0
- self.total_intensity[i] = np.sum(
- self.image[i], initial=0, where=mask)
- self.num_lit_px[i] = np.sum(
- self.image[i] > self.threshold, initial=0, where=mask)
- self.num_unmasked_px[i] = np.sum(mask)
-
- def source_name(self, karabo_id, channel):
- return f"{karabo_id}/LITPX/{channel}"