Port batch image export onto the sras_viewer package split

origin/main split sras_viewer.py into the sras_viewer/ package (dialogs,
main_window, common, canvases) after the batch-export feature was built
against the old monolith, so merging origin/main into main lost the feature
to the sras_viewer.py deletion. Re-add it in the new structure:
BatchExportDialog in dialogs.py, a Jobs.EXPORT job key in common.py, and
the menu action/worker wiring in main_window.py, following the Jobs-key
and dialog-class conventions the split already established rather than the
old ad hoc "main" progress-key naming the original commit used.

Also carries forward two test fixes bundled in the original batch-export
commit that the parallel pytest conversion (007089d) had ported from
tools/test_refactor.py without them: the int16-vs-float32 accumulator
expectation in test_sras_average, and asserting the sras_average.py
subprocess calls actually succeed.
This commit is contained in:
Thomas Ales [M S E]
2026-08-10 18:58:56 -05:00
parent 105b9514a5
commit aca501ae5c
4 changed files with 275 additions and 16 deletions
+1
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@@ -60,6 +60,7 @@ class Jobs:
COMPUTE = "compute" COMPUTE = "compute"
DC_PRECOMPUTE = "dc_precompute" DC_PRECOMPUTE = "dc_precompute"
BATCH = "batch" BATCH = "batch"
EXPORT = "export"
# The alignment wizard's three background steps: fetching each angle's CH4 # The alignment wizard's three background steps: fetching each angle's CH4
# image for the mask stack, registering the angles, and writing the aligned # image for the mask stack, registering the angles, and writing the aligned
# export. Separate keys because a retry of one must not be blocked by # export. Separate keys because a retry of one must not be blocked by
+140 -4
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@@ -8,15 +8,20 @@ mask-overlay editor plus the crop and export steps.
from pathlib import Path from pathlib import Path
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QButtonGroup, QCheckBox, QDialog, QDialogButtonBox, QFileDialog, QButtonGroup, QCheckBox, QDialog, QDialogButtonBox, QDoubleSpinBox,
QGroupBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QRadioButton, QFileDialog, QGridLayout, QGroupBox, QHBoxLayout, QLabel, QLineEdit,
QScrollArea, QSpinBox, QVBoxLayout, QWidget, QMessageBox, QPushButton, QRadioButton, QScrollArea, QSpinBox,
QVBoxLayout, QWidget,
) )
from sras_compute import PYFFTW_AVAILABLE from sras_compute import PYFFTW_AVAILABLE
from sras_format import CH1_IDX, CH3_IDX, CH4_IDX, CH_NAMES from sras_format import CH1_IDX, CH3_IDX, CH4_IDX, CH_NAMES
from sras_workers import ExportChannel
from .common import CH_LABELS, VELOCITY_MODE_IDX, _CSS_HINT, _CSS_WARN, _group, _make_dspin, _wrap_label from .common import (
CH_LABELS, VELOCITY_MODE_IDX, _CHANNEL_DISPLAY, _CSS_HINT, _CSS_WARN,
_SPIN_MIN_W, _form, _group, _make_dspin, _wrap_label,
)
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
@@ -240,6 +245,137 @@ class RowAverageFftOptionsDialog(QDialog):
return self._spin_threshold.value() return self._spin_threshold.value()
# ---------------------------------------------------------------------------
# Batch export dialog (Export -> Batch Export Images...)
# ---------------------------------------------------------------------------
class BatchExportDialog(QDialog):
"""Configure a batch PNG export of DC/RF/Velocity maps across every angle
of the currently open file.
Each channel's colorbar range is entered here and held fixed for every
exported angle (rather than auto-scaled per image, today's live-view
default) so the exported images are directly comparable to each other.
"""
# (ch_idx, is_velocity, label, colorbar unit, filename tag)
_ROWS = [
(CH1_IDX, False, CH_LABELS[CH1_IDX], _CHANNEL_DISPLAY[CH1_IDX][2],
CH_NAMES[CH1_IDX]),
(CH3_IDX, False, CH_LABELS[CH3_IDX], _CHANNEL_DISPLAY[CH3_IDX][2],
CH_NAMES[CH3_IDX]),
(CH4_IDX, False, CH_LABELS[CH4_IDX], _CHANNEL_DISPLAY[CH4_IDX][2],
CH_NAMES[CH4_IDX]),
(CH1_IDX, True, CH_LABELS[VELOCITY_MODE_IDX],
_CHANNEL_DISPLAY[VELOCITY_MODE_IDX][2], CH_NAMES[VELOCITY_MODE_IDX]),
]
# DC is cheap and precomputed on load; CH1/Velocity need a per-pixel FFT
# that can take minutes, so don't default to exporting them (same
# rationale as SrasViewerWindow._on_load_done's channel default).
_DEFAULT_CHECKED = {CH3_IDX, CH4_IDX}
def __init__(self, parent, *, default_dir: str, default_prefix: str,
default_ranges: dict[tuple[int, bool], tuple[float, float]]):
super().__init__(parent)
self.setWindowTitle("Batch Export Images")
self.setModal(True)
self.setMinimumWidth(460)
layout = QVBoxLayout(self)
# ---- Output ------------------------------------------------------
grp_out, ol = _group("Output")
dir_row = QHBoxLayout()
self._edit_dir = QLineEdit(default_dir)
btn_browse = QPushButton("Browse…")
btn_browse.clicked.connect(self._on_browse)
dir_row.addWidget(self._edit_dir)
dir_row.addWidget(btn_browse)
out_form = _form()
out_form.addRow("Folder:", dir_row)
self._edit_prefix = QLineEdit(default_prefix)
out_form.addRow("File prefix:", self._edit_prefix)
ol.addLayout(out_form)
layout.addWidget(grp_out)
# ---- Channels ------------------------------------------------------
grp_ch, cl = _group("Channels (fixed range, applied to every angle)")
grid = QGridLayout()
grid.setHorizontalSpacing(8)
grid.setVerticalSpacing(6)
grid.addWidget(_wrap_label("min:", _CSS_HINT), 0, 1)
grid.addWidget(_wrap_label("max:", _CSS_HINT), 0, 2)
self._rows: list[tuple[QCheckBox, QDoubleSpinBox, QDoubleSpinBox]] = []
for i, (ch_idx, is_velocity, label, unit, _tag) in enumerate(self._ROWS, 1):
chk = QCheckBox(label + (f" [{unit}]" if unit else ""))
chk.setChecked(not is_velocity and ch_idx in self._DEFAULT_CHECKED)
vmin, vmax = default_ranges.get((ch_idx, is_velocity), (0.0, 1.0))
spin_min, spin_max = QDoubleSpinBox(), QDoubleSpinBox()
for spin, val in ((spin_min, vmin), (spin_max, vmax)):
spin.setRange(-1e9, 1e9)
spin.setDecimals(4)
spin.setMinimumWidth(_SPIN_MIN_W)
spin.setValue(val)
grid.addWidget(chk, i, 0)
grid.addWidget(spin_min, i, 1)
grid.addWidget(spin_max, i, 2)
self._rows.append((chk, spin_min, spin_max))
cl.addLayout(grid)
layout.addWidget(grp_ch)
# ---- Buttons --------------------------------------------------
buttons = QDialogButtonBox()
buttons.addButton("Export", QDialogButtonBox.ButtonRole.AcceptRole
).clicked.connect(self.accept)
buttons.addButton("Cancel", QDialogButtonBox.ButtonRole.RejectRole
).clicked.connect(self.reject)
layout.addWidget(buttons)
def _on_browse(self):
d = QFileDialog.getExistingDirectory(
self, "Select Output Folder", self._edit_dir.text())
if d:
self._edit_dir.setText(d)
def accept(self):
"""Validate before closing — Cancel bypasses this entirely."""
if not self.get_prefix():
QMessageBox.warning(self, "Batch Export", "Enter a file prefix.")
return
if not self.get_output_dir():
QMessageBox.warning(self, "Batch Export", "Choose an output folder.")
return
selected = self.get_selected_channels()
if not selected:
QMessageBox.warning(
self, "Batch Export", "Select at least one channel to export.")
return
for ch in selected:
if not ch.vmin < ch.vmax:
QMessageBox.warning(
self, "Batch Export", f"{ch.label}: min must be less than max.")
return
super().accept()
def get_output_dir(self) -> str:
return self._edit_dir.text().strip()
def get_prefix(self) -> str:
return self._edit_prefix.text().strip()
def get_selected_channels(self) -> list[ExportChannel]:
result = []
for (chk, spin_min, spin_max), (ch_idx, is_velocity, label, unit, tag) in zip(
self._rows, self._ROWS):
if chk.isChecked():
result.append(ExportChannel(
ch_idx=ch_idx, is_velocity=is_velocity,
vmin=spin_min.value(), vmax=spin_max.value(),
label=label, unit=unit, tag=tag))
return result
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# Export Fused ROI dialog # Export Fused ROI dialog
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
+122 -5
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@@ -9,8 +9,8 @@ from PyQt6.QtCore import QObject, QSettings, QSignalBlocker, Qt, QThread
from PyQt6.QtGui import QAction from PyQt6.QtGui import QAction
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QApplication, QCheckBox, QComboBox, QDialog, QFileDialog, QFrame, QApplication, QCheckBox, QComboBox, QDialog, QFileDialog, QFrame,
QHBoxLayout, QLabel, QMainWindow, QProgressDialog, QPushButton, QHBoxLayout, QLabel, QMainWindow, QMessageBox, QProgressDialog,
QSizePolicy, QSpinBox, QSplitter, QVBoxLayout, QWidget, QPushButton, QSizePolicy, QSpinBox, QSplitter, QVBoxLayout, QWidget,
) )
import sras_compute as compute import sras_compute as compute
@@ -19,11 +19,12 @@ from sras_compute import (
load_manual_alignment, save_manual_alignment, sidecar_path, load_manual_alignment, save_manual_alignment, sidecar_path,
) )
from sras_format import ( from sras_format import (
CH3_IDX, CH4_IDX, CH_NAMES, SrasFile, mv_to_adc, CH1_IDX, CH3_IDX, CH4_IDX, CH_NAMES, SrasFile, mv_to_adc,
_FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC, _FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC,
) )
from sras_workers import ( from sras_workers import (
BatchCacheWorker, ComputeWorker, DcPrecomputeWorker, LoadWorker, BatchCacheWorker, BatchExportWorker, ComputeWorker, DcPrecomputeWorker,
LoadWorker,
) )
from .canvases import ImageCanvas, WaveformCanvas from .canvases import ImageCanvas, WaveformCanvas
@@ -35,7 +36,8 @@ from .common import (
) )
from .align_wizard import AlignmentWizard from .align_wizard import AlignmentWizard
from .dialogs import ( from .dialogs import (
FftOptionsDialog, FusedRoiExportDialog, RowAverageFftOptionsDialog, BatchExportDialog, FftOptionsDialog, FusedRoiExportDialog,
RowAverageFftOptionsDialog,
) )
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
@@ -85,6 +87,10 @@ class SrasViewerWindow(QMainWindow):
# Convert menu: batch DC/FFT compute-and-store (v6 -> v7) # Convert menu: batch DC/FFT compute-and-store (v6 -> v7)
self._batch_errors: list[str] = [] self._batch_errors: list[str] = []
# Export menu: batch image export
self._export_errors: list[str] = []
self._export_ok_count: int = 0
# Display-only settings (colormap, grating) never trigger a # Display-only settings (colormap, grating) never trigger a
# recompute — they're applied to cached data on redraw. DC images # recompute — they're applied to cached data on redraw. DC images
# (CH3/CH4) are cheap and precomputed for every angle in the # (CH3/CH4) are cheap and precomputed for every angle in the
@@ -480,6 +486,15 @@ class SrasViewerWindow(QMainWindow):
self._batch_fft_rowavg_act.triggered.connect(self._on_batch_compute_row_avg) self._batch_fft_rowavg_act.triggered.connect(self._on_batch_compute_row_avg)
convert_menu.addAction(self._batch_fft_rowavg_act) convert_menu.addAction(self._batch_fft_rowavg_act)
export_menu = menubar.addMenu("&Export")
self._batch_export_act = QAction("&Batch Export Images…", self)
self._batch_export_act.setStatusTip(
"Export DC/RF/Velocity map PNGs for every angle of the open "
"file, with a fixed colorbar range per channel.")
self._batch_export_act.setEnabled(False)
self._batch_export_act.triggered.connect(self._on_batch_export)
export_menu.addAction(self._batch_export_act)
# ------------------------------------------------------------------ # ------------------------------------------------------------------
# Drag-and-drop # Drag-and-drop
# ------------------------------------------------------------------ # ------------------------------------------------------------------
@@ -702,6 +717,8 @@ class SrasViewerWindow(QMainWindow):
self._wizard_act.setEnabled( self._wizard_act.setEnabled(
has_file and s.n_angles > 1 and self._align_wizard is None) has_file and s.n_angles > 1 and self._align_wizard is None)
self.chk_aligned_view.setEnabled(enabled and self._alignment_result is not None) self.chk_aligned_view.setEnabled(enabled and self._alignment_result is not None)
self._batch_export_act.setEnabled(has_file and not self._job_running(Jobs.EXPORT))
self._update_roi_ui() self._update_roi_ui()
def _on_channel_changed(self): def _on_channel_changed(self):
@@ -1538,6 +1555,106 @@ class SrasViewerWindow(QMainWindow):
self._batch_fft_act.setEnabled(True) self._batch_fft_act.setEnabled(True)
self._batch_fft_rowavg_act.setEnabled(True) self._batch_fft_rowavg_act.setEnabled(True)
# ------------------------------------------------------------------
# Export menu: batch image export
# ------------------------------------------------------------------
def _export_default_ranges(self) -> dict[tuple[int, bool], tuple[float, float]]:
"""Best-effort default min/max per exportable channel, from whatever
is already cached — this must never trigger a fresh compute just to
seed the dialog (CH1/Velocity in particular can be expensive)."""
s = self._sras
ranges: dict[tuple[int, bool], tuple[float, float]] = {}
for ch_idx, precomputed in ((CH3_IDX, s.precomputed_dc3_mv),
(CH4_IDX, s.precomputed_dc4_mv)):
arrays = [self._dc_cache.get((a, ch_idx)) for a in range(s.n_angles)]
arrays = [a for a in arrays if a is not None]
if not arrays:
arrays = [a for a in precomputed if a is not None]
if arrays:
ranges[(ch_idx, False)] = (
float(min(a.min() for a in arrays)),
float(max(a.max() for a in arrays)))
freq_arrays = list(self._fft_cache.values())
if not freq_arrays:
freq_arrays = [a for a in s.precomputed_freq_mhz if a is not None]
if freq_arrays:
fmin = float(min(a.min() for a in freq_arrays))
fmax = float(max(a.max() for a in freq_arrays))
ranges[(CH1_IDX, False)] = (fmin, fmax)
grating = self.spin_grating_um.value()
ranges[(CH1_IDX, True)] = (fmin * grating, fmax * grating)
return ranges
def _on_batch_export(self):
if self._sras is None or self._job_running(Jobs.EXPORT):
return
s = self._sras
dlg = BatchExportDialog(
self, default_dir=str(s.path.parent), default_prefix=s.path.stem,
default_ranges=self._export_default_ranges())
if dlg.exec() != QDialog.DialogCode.Accepted:
return
output_dir = dlg.get_output_dir()
try:
Path(output_dir).mkdir(parents=True, exist_ok=True)
except OSError as exc:
QMessageBox.warning(
self, "Batch Export", f"Could not create output folder:\n{exc}")
return
channels = dlg.get_selected_channels()
self._export_errors = []
self._export_ok_count = 0
worker = BatchExportWorker(
s, channels, output_dir, dlg.get_prefix(),
cmap=self.combo_cmap.currentText(),
apply_bg_sub=self.chk_bg_sub.isChecked(),
dc_threshold_mv=self.spin_threshold_mv.value(),
n_fft=self._current_n_fft(), grating_um=self.spin_grating_um.value())
started = self._run_worker(
Jobs.EXPORT, worker,
connect=(
("progress", lambda pct: self._set_progress(Jobs.EXPORT, pct)),
("file_done", self._on_export_file_done),
("finished", self._on_export_finished),
),
on_done=self._after_export,
)
if not started:
return # a second trigger snuck in while the dialog was open
self._batch_export_act.setEnabled(False)
self._show_progress(
Jobs.EXPORT, f"Exporting images to {output_dir}…", maximum=100)
def _on_export_file_done(self, path: str, err: str):
if err:
self._export_errors.append(f"{Path(path).name if path else '?'} — {err}")
else:
self._export_ok_count += 1
self._show_progress(Jobs.EXPORT, f"Wrote {Path(path).name}…")
def _on_export_finished(self):
self._close_progress(Jobs.EXPORT)
n_ok = self._export_ok_count
n_failed = len(self._export_errors)
if n_failed:
summary = (f"Batch export: {n_ok} image(s) written, {n_failed} "
f"failed: {'; '.join(self._export_errors)}")
else:
summary = f"Batch export: {n_ok} image(s) written."
self.statusBar().showMessage(summary)
self._export_errors = []
def _after_export(self):
self._update_controls_enabled(self._sras is not None)
# ------------------------------------------------------------------ # ------------------------------------------------------------------
# Fusion: angle alignment # Fusion: angle alignment
# ------------------------------------------------------------------ # ------------------------------------------------------------------
+8 -3
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@@ -327,21 +327,26 @@ def test_sras_average(tmp_path):
assert np.array_equal(avg.background, SrasFile(str(src)).background), \ assert np.array_equal(avg.background, SrasFile(str(src)).background), \
"background preserved" "background preserved"
src_data = meta["data"] src_data = meta["data"]
expect0 = src_data[0][:, :, 0:4, :].astype(np.float32).mean(axis=2).astype(np.int16) # int16 (not float32) before .mean(): matches average_rows' own
# float64-accumulator behavior for integer input, so this doesn't
# drift from what average_rows actually guarantees.
expect0 = src_data[0][:, :, 0:4, :].astype(np.int16).mean(axis=2).astype(np.int16)
assert np.array_equal(np.asarray(avg.data[0])[:, :, 0, :], expect0), \ assert np.array_equal(np.asarray(avg.data[0])[:, :, 0, :], expect0), \
"first averaged group equals the mean of its 4 source frames" "first averaged group equals the mean of its 4 source frames"
# Remainder handling: 12 frames / 5 -> 2 full groups + 1 partial. # Remainder handling: 12 frames / 5 -> 2 full groups + 1 partial.
dst2 = tmp_path / "legacy_v4_avg5.sras" dst2 = tmp_path / "legacy_v4_avg5.sras"
subprocess.run([sys.executable, str(REPO / "sras_average.py"), proc2 = subprocess.run([sys.executable, str(REPO / "sras_average.py"),
str(src), str(dst2), "--n", "5"], str(src), str(dst2), "--n", "5"],
capture_output=True, text=True, cwd=REPO) capture_output=True, text=True, cwd=REPO)
assert proc2.returncode == 0, (proc2.stderr or proc2.stdout).strip()[-200:]
assert list(SrasFile(str(dst2)).n_frames) == [3, 3], \ assert list(SrasFile(str(dst2)).n_frames) == [3, 3], \
"partial trailing group kept by default" "partial trailing group kept by default"
dst3 = tmp_path / "legacy_v4_avg5d.sras" dst3 = tmp_path / "legacy_v4_avg5d.sras"
subprocess.run([sys.executable, str(REPO / "sras_average.py"), proc3 = subprocess.run([sys.executable, str(REPO / "sras_average.py"),
str(src), str(dst3), "--n", "5", "--discard-remainder"], str(src), str(dst3), "--n", "5", "--discard-remainder"],
capture_output=True, text=True, cwd=REPO) capture_output=True, text=True, cwd=REPO)
assert proc3.returncode == 0, (proc3.stderr or proc3.stdout).strip()[-200:]
assert list(SrasFile(str(dst3)).n_frames) == [2, 2], \ assert list(SrasFile(str(dst3)).n_frames) == [2, 2], \
"--discard-remainder drops the partial group" "--discard-remainder drops the partial group"