From bfcd3a8c6a06541f745fadd7e3ecaea0ead5924e Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Fri, 17 Dec 2021 16:02:16 +0100
Subject: [PATCH] Specify frameFilter without eval
---
src/calng/base_correction.py | 88 ++++++++++++++++++++++++++++++------
1 file changed, 75 insertions(+), 13 deletions(-)
diff --git a/src/calng/base_correction.py b/src/calng/base_correction.py
index 033ba715..b3243e30 100644
--- a/src/calng/base_correction.py
+++ b/src/calng/base_correction.py
@@ -180,7 +180,8 @@ class BaseCorrection(PythonDevice):
"dataFormat.outputAxisOrder",
"dataFormat.outputImageDtype",
"dataFormat.overrideInputAxisOrder",
- "frameFilter",
+ "frameFilter.type",
+ "frameFilter.spec",
"preview.enable",
"preview.index",
"preview.selectionMode",
@@ -266,7 +267,7 @@ class BaseCorrection(PythonDevice):
.defaultValue([])
.commit(),
- STRING_ELEMENT(expected)
+ NODE_ELEMENT(expected)
.key("frameFilter")
.displayedName("Frame filter")
.description(
@@ -274,15 +275,46 @@ class BaseCorrection(PythonDevice):
"filter will be discarded before any processing happens and will not "
"get to dataOutput or preview. Note that this filter goes by frame "
"index rather than cell ID or pulse ID; set accordingly. Handle with "
- "care - an invalid filter can prevent all processing. The filter is "
- "specified as a string which is evaluated into numpy uint16 array. A "
- "valid filter could for eaxmple be 'np.arange(0, 352, 2)'."
+ "care - an invalid filter can prevent all processing. How the filter "
+ "is specified depends on frameFilter.type. See frameFilter.current to "
+ "inspect the currently set frame filter array (if any)."
+ )
+ .commit(),
+
+ STRING_ELEMENT(expected)
+ .key("frameFilter.type")
+ .displayedName("Filter definition type")
+ .description(
+ "Controls how frameFilter.spec is used. The default value of 'none' "
+ "means that no filter is set (regardless of frameFilter.spec). "
+ "'arange' allows between one and three integers separated by ',' which "
+ "are parsed and passed directly to numpy.arange. 'commaseparated' "
+ "reads a list of integers separated by commas."
)
+ .options("none,arange,commaseparated")
+ .assignmentOptional()
+ .defaultValue("none")
+ .reconfigurable()
+ .commit(),
+
+ STRING_ELEMENT(expected)
+ .key("frameFilter.spec")
.assignmentOptional()
.defaultValue("")
.reconfigurable()
.commit(),
+ VECTOR_UINT32_ELEMENT(expected)
+ .key("frameFilter.current")
+ .displayedName("Current filter")
+ .description(
+ "This read-only value is used to display the contents of the current "
+ "frame filter. An empty array means no filtering is done."
+ )
+ .readOnly()
+ .initialValue([])
+ .commit(),
+
UINT32_ELEMENT(expected)
.key("outputShmemBufferSize")
.displayedName("Output buffer size limit")
@@ -787,20 +819,50 @@ class BaseCorrection(PythonDevice):
self.log.DEBUG(f"Corrections for preview: {str(preview)}")
def _update_frame_filter(self):
- """Parse frameFilter string (if set) and update cached filter array. Will set
+ """Parse frameFilter string (if set) and update cached filter array. May update
dataFormat.filteredFrames, so one will typically want to call _update_buffers
afterwards."""
- filter_string = self.get("frameFilter")
- if filter_string.strip() == "":
+ # TODO: add some validation to preReconfigure
+ self.log.DEBUG("Updating frame filter")
+ filter_type = self.get("frameFilter.type")
+ filter_string = self.get("frameFilter.spec")
+
+ if filter_type == "none" or filter_string.strip() == "":
self._frame_filter = None
+ elif filter_type == "arange":
+ try:
+ numbers = tuple(int(part) for part in filter_string.split(","))
+ except (ValueError, TypeError):
+ self.log_status_warn(
+ f"Invalid frame filter specification: {filter_string}"
+ )
+ else:
+ self._frame_filter = np.arange(*numbers, dtype=np.uint16)
+ elif filter_type == "commaseparated":
+ try:
+ self._frame_filter = np.fromstring(
+ filter_string, sep=",", dtype=np.uint16
+ )
+ except ValueError:
+ # note: only in the future will numpy actually give ValueError
+ self.log_status_warn(
+ f"Invalid frame filter specification: {filter_string}"
+ )
+ else:
+ self.log_status_warn(f"Invalid frame filter type '{filter_type}'")
+
+ if self._frame_filter is None:
self.set("dataFormat.filteredFrames", self.get("dataFormat.memoryCells"))
+ self.set("frameFilter.current", [])
else:
- self._frame_filter = np.array(eval(filter_string), dtype=np.uint16)
self.set("dataFormat.filteredFrames", self._frame_filter.size)
- if self._frame_filter.min() < 0 or self._frame_filter.max() >= self.get(
- "dataFormat.memoryCells"
- ):
- self.log_status_warn("Invalid frame filter set, expect exceptions!")
+ self.set("frameFilter.current", list(map(int, self._frame_filter)))
+
+ if self._frame_filter is not None and (
+ self._frame_filter.min() < 0
+ or self._frame_filter.max() >= self.get("dataFormat.memoryCells")
+ ):
+ self.log_status_warn("Invalid frame filter set, expect exceptions!")
def _update_buffers(self):
"""(Re)initialize buffers / kernel runner according to expected data shapes"""
--
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