diff --git a/CLAUDE.md b/CLAUDE.md index b78ba65..b548069 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -272,7 +272,7 @@ handles stock sequences and third-party ones are what force a manual rebuild. scan a person should look at, which is what that verdict means. No shipped example does it; the branch exists so a future one is visible rather than quietly resolved. -- The corpus stands at 677 third-party, 276 stock and 31 unrecognized, pinned by +- The corpus stands at 701 third-party, 299 stock and 31 unrecognized, pinned by `test_the_shipped_examples_are_accounted_for_apart_from_a_pinned_few`. `tse_crusher` (`Flair axial low SAR`) is labelled `USER` and so reports third-party; `fl3d_rd` (`vessels_head`) is labelled `SIEMENS` and is also in @@ -515,6 +515,24 @@ before/after pair is the only way to learn where a printed value is stored -- real difference is hardware: `aRxCoilSelectData[1].aFFT_SCALE` has 58 entries on P1 and 20 on P2, on the one scan using a second coil array. A generator moving a protocol between scanners must not copy that across. +- **A step in the running order need not run anything.** `EdfPauseStep` is an + instruction an operator put between scans -- "Count down with RA to start of + scan", "Pause for saliva collection", "Do NOT add Raw Filter to 3D MPR" -- + carrying an `EdfMeasurementStepContent` with injector fields and no protocol + child. Eleven of `CHR-MDD`'s thirty-four steps are pauses, and the reader + raised on all three archives that arrived with them. They are named, they are + in the chain, and the PDF does not print them as scans, so anything walking + *scans* skips them: `Step.is_pause` reads the instance kind, `runs_a_protocol` + reads the content, and a test asserts the two always agree because either + alone could be wrong. +- **A printout carries fewer digits than the protocol.** One scan prints + `TE 1 = 54 ms` for a stored `54.16`, so writing the printed value back drops + 0.16 ms. `build.agrees_at_printed_precision` treats a printed value as + matching when the stored one rounds to it at the precision actually printed; + without it, driving an archive from its own PDF degrades it. +- **Strip a printed unit only after whitespace.** Matching it anywhere turns + `RMS` into `R`, because `MS` is a unit and the comparison is + case-insensitive -- which then fails to resolve as an `Averaging` choice. - **A readable archive can hold no protocols at all.** Exporting an empty folder node rather than the protocol tree yields a valid SQLite file with the directory scaffolding, a `Root` label and nothing else -- five diff --git a/examples/XA60/31P CSI 20230503 NOE.exar1 b/examples/XA60/31P CSI 20230503 NOE.exar1 new file mode 100755 index 0000000..01ea0fe Binary files /dev/null and b/examples/XA60/31P CSI 20230503 NOE.exar1 differ diff --git a/examples/XA60/31P CSI 20230503 NOE.pdf b/examples/XA60/31P CSI 20230503 NOE.pdf index 762a0d2..6ed7c0f 100644 Binary files a/examples/XA60/31P CSI 20230503 NOE.pdf and b/examples/XA60/31P CSI 20230503 NOE.pdf differ diff --git a/examples/XA60/CHR-MDD.exar1 b/examples/XA60/CHR-MDD.exar1 new file mode 100755 index 0000000..fa822a3 Binary files /dev/null and b/examples/XA60/CHR-MDD.exar1 differ diff --git a/examples/XA60/CHR-MDD.pdf b/examples/XA60/CHR-MDD.pdf new file mode 100755 index 0000000..ea7f63b Binary files /dev/null and b/examples/XA60/CHR-MDD.pdf differ diff --git a/examples/XA60/ZMK23 with Physio.exar1 b/examples/XA60/ZMK23 with Physio.exar1 new file mode 100755 index 0000000..4ec3abc Binary files /dev/null and b/examples/XA60/ZMK23 with Physio.exar1 differ diff --git a/examples/XA60/ZMK23 with Physio.pdf b/examples/XA60/ZMK23 with Physio.pdf new file mode 100644 index 0000000..60a43bd Binary files /dev/null and b/examples/XA60/ZMK23 with Physio.pdf differ diff --git a/src/siemens_protocol/exar/archive.py b/src/siemens_protocol/exar/archive.py index ab7dac6..736f452 100644 --- a/src/siemens_protocol/exar/archive.py +++ b/src/siemens_protocol/exar/archive.py @@ -48,6 +48,16 @@ #: Instance types, as ``Instance.InstanceType`` spells them. PROGRAM = "EdfProgram" MEASUREMENT_STEP = "EdfMeasurementStep" + +#: A step in the running order that acquires nothing. Operators put pause and +#: instruction steps between scans -- "Count down with RA to start of scan", +#: "Pause for saliva collection" -- and the console gives them their own +#: instance type. They are common in real clinical trees, so the running order +#: mixes both kinds and anything walking *scans* has to skip these. +PAUSE_STEP = "EdfPauseStep" + +#: Both kinds that appear in a program's running order. +STEP_KINDS = (MEASUREMENT_STEP, PAUSE_STEP) PROTOCOL = "EdfProtocol" STRING = "EdfString" @@ -239,6 +249,36 @@ class Step: name: str protocols: list[Protocol] = field(default_factory=list) + @property + def is_pause(self) -> bool: + """Return whether this step is an instruction rather than an acquisition. + + Returns + ------- + bool + ``True`` for an ``EdfPauseStep``. + """ + return self.instance.kind == PAUSE_STEP + + @property + def runs_a_protocol(self) -> bool: + """Return whether this step acquires anything. + + A measurement step need not hold a protocol. Operators put pause and + instruction steps in the running order -- "Count down with RA to start + of scan", "Pause for saliva collection", "Do NOT add Raw Filter to 3D + MPR" -- and those carry an ``EdfMeasurementStepContent`` with injector + fields and no protocol child. They are common in real clinical trees + and the PDF does not print them as scans, so anything walking scans + must skip them rather than assume every step has one. + + Returns + ------- + bool + ``True`` when the step holds at least one protocol. + """ + return bool(self.protocols) + @property def protocol(self) -> Protocol: """Return the step's single protocol. @@ -251,7 +291,9 @@ def protocol(self) -> Protocol: Raises ------ ValueError - If the step holds no protocol at all. + If the step holds no protocol at all, which is a legitimate state + -- see :attr:`runs_a_protocol` -- so callers sweeping an archive + should test that first rather than catching this. """ if not self.protocols: raise ValueError(f"measurement step {self.name!r} holds no protocol") diff --git a/src/siemens_protocol/exar/build.py b/src/siemens_protocol/exar/build.py index cea9c34..bd33089 100644 --- a/src/siemens_protocol/exar/build.py +++ b/src/siemens_protocol/exar/build.py @@ -32,7 +32,7 @@ #: Units the card prints beside a value and the protocol does not store. UNIT_SUFFIX = re.compile( - r"\s*(ms|s|mm|cm|deg|degree|degrees|Hz|Hz/Px|kHz|%|TRs|TR|min|sec|mT/m|ppm)\s*$", + r"\s+(ms|s|mm|cm|deg|degree|degrees|Hz|Hz/Px|kHz|%|TRs|TR|min|sec|mT/m|ppm)\s*$", re.I, ) @@ -52,8 +52,10 @@ def printed_value(text: Any) -> Any: """ if not isinstance(text, str): return text - # Some values carry two: "5.0 mm" is one, "24 TRs" is one, and a printed - # angle is "360 degrees". Strip repeatedly rather than assume a single unit. + # The unit has to follow whitespace. Matching it anywhere turns "RMS" into + # "R", because "MS" is a unit and the comparison is case-insensitive -- + # which then fails to resolve as an Averaging choice. Strip repeatedly, + # since a value can carry more than one suffix. stripped = text.strip() while True: shorter = UNIT_SUFFIX.sub("", stripped).strip() @@ -180,24 +182,65 @@ def apply_protocol(archive: Archive, parsed: MappingType[str, Any]) -> BuildRepo What was written, refused and inherited. """ report = BuildReport() + # A pause step carries no protocol and the PDF does not print it as a scan, + # so it can never be the counterpart of one. steps: dict[str, list[Any]] = {} for step in archive.steps: - steps.setdefault(step.name, []).append(step) + if step.runs_a_protocol: + steps.setdefault(step.name, []).append(step) - seen: set[str] = set() + scans: dict[str, list[Any]] = {} for scan in parsed.get("scans", []): - name = scan.get("name", "") - found = steps.get(name, []) - if len(found) != 1: - report.unmatched.append(name) + scans.setdefault(scan.get("name", ""), []).append(scan) + + seen: set[str] = set() + for name, printed in scans.items(): + held = steps.get(name, []) + # A name repeats: a protocol may run four scans called Localizer. Pair + # them in running order, which both sides preserve -- but only when the + # two sides agree on how many there are. Otherwise which is which is a + # guess, and guessing would write one scan's values into another. + if not held or len(held) != len(printed): + report.unmatched.extend(name for _ in printed) continue seen.add(name) - report.matched.append(name) - _apply_scan(archive, found[0], scan, report) + for step, scan in zip(held, printed): + report.matched.append(name) + _apply_scan(archive, step, scan, report) report.untouched = [n for n in steps if n not in seen] return report +def agrees_at_printed_precision(printed: str, stored: Any) -> bool: + """Return whether a stored value and a printed one are the same number. + + A printout carries fewer digits than the protocol: one scan prints + ``TE 1 = 54 ms`` for a stored 54.16. Writing the printed value back would + quietly drop 0.16 ms, so a printed value is treated as agreeing when the + stored one rounds to it at the precision actually printed. + + Parameters + ---------- + printed : str + The value as the card prints it, units already removed. + stored : Any + What the protocol holds. + + Returns + ------- + bool + ``True`` when the two are the same number to the printed precision. + """ + if not isinstance(stored, (int, float)) or isinstance(stored, bool): + return False + try: + wanted = float(printed) + except (TypeError, ValueError): + return False + _whole, _, fraction = str(printed).strip().partition(".") + return round(float(stored), len(fraction)) == wanted + + def _moved(record: patch.Applied) -> bool: """Return whether a written record actually changed anything. @@ -242,7 +285,16 @@ def _apply_scan( if mapping is None: report.inherited[label] += 1 continue - requests[label] = printed_value(value) + wanted = printed_value(value) + entry = ( + step.protocol.preview.get(mapping.preview_path) + if mapping.preview_path is not None + else None + ) + if entry is not None and agrees_at_printed_precision(wanted, entry.value): + report.unchanged += 1 + continue + requests[label] = wanted if not requests: return document, applied, skipped = patch.patch_document(step.protocol, requests, step=step.name) diff --git a/src/siemens_protocol/exar/patch.py b/src/siemens_protocol/exar/patch.py index e722c12..6fc0066 100644 --- a/src/siemens_protocol/exar/patch.py +++ b/src/siemens_protocol/exar/patch.py @@ -1298,6 +1298,17 @@ def apply(archive: Archive, changes: MappingType[str, MappingType[str, Any]]) -> ) continue step = found[0] + if not step.runs_a_protocol: + for label, value in requests.items(): + manifest.skipped.append( + Skipped( + step=name, + label=label, + value=value, + reason="that step is a pause and holds no protocol", + ) + ) + continue protocol = step.protocol document, applied, skipped = patch_document(protocol, requests, step=name) manifest.applied.extend(applied) diff --git a/src/siemens_protocol/exar/validate.py b/src/siemens_protocol/exar/validate.py index 33703f3..c34fadc 100644 --- a/src/siemens_protocol/exar/validate.py +++ b/src/siemens_protocol/exar/validate.py @@ -20,7 +20,7 @@ from typing import Any from . import envelope -from .archive import MEASUREMENT_STEP, Archive +from .archive import STEP_KINDS, Archive from .generate import NO_GUID, STEP_KEYED_MAPS #: Matches a GUID as these payloads spell one. @@ -106,7 +106,7 @@ def _running_order(archive: Archive, document: dict[str, Any]) -> list[str]: # derived by walking the chain, so comparing the two would be circular: a # chain that stops early would agree with itself and the break would show # up only as unrelated complaints about the maps. - existing = sum(1 for i in archive.instances.values() if i.kind == MEASUREMENT_STEP) + existing = sum(1 for i in archive.instances.values() if i.kind in STEP_KINDS) if len(order) != existing: found.append(f"link chain covers {len(order)} steps but {existing} exist") if order and document.get("FirstStepId") != order[0]: @@ -183,10 +183,9 @@ def _parents(archive: Archive) -> list[str]: program = archive.program found = [] for step in archive.steps: - expected = { - "protocol": (step.protocol.instance, step.instance.element_id), - "step": (step.instance, program.element_id), - } + expected = {"step": (step.instance, program.element_id)} + if step.runs_a_protocol: + expected["protocol"] = (step.protocol.instance, step.instance.element_id) holder = archive.by_element.get(step.instance.label_element_id) if holder is not None: expected["label"] = (holder, step.instance.element_id) diff --git a/tests/golden/XA60-31P CSI 20230503 NOE.json b/tests/golden/XA60-31P CSI 20230503 NOE.json index 0cfdbf2..aebb8cf 100644 --- a/tests/golden/XA60-31P CSI 20230503 NOE.json +++ b/tests/golden/XA60-31P CSI 20230503 NOE.json @@ -211,7 +211,7 @@ "LR Balancing": "Off" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" @@ -461,7 +461,7 @@ "Excitation": "Non-sel." }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" @@ -689,7 +689,7 @@ "Excitation": "Non-sel." }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Correction Factor": "1.00", @@ -885,7 +885,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Correction Factor": "1.00", @@ -1035,7 +1035,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Correction Factor": "1.00", @@ -1185,7 +1185,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Correction Factor": "1.00", @@ -1335,7 +1335,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Correction Factor": "1.00", @@ -1485,7 +1485,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" @@ -1522,9 +1522,9 @@ "name": "head_csi_fid", "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", "header": { - "ta": "12:54 min", + "ta": "36:24 min", "coil_selection": "Auto", - "voxel_size_mm": "25.0×25.0×25.0", + "voxel_size_mm": "50.0×50.0×36.0", "rel_snr": "1.00", "sequence": "csi_fid" }, @@ -1552,55 +1552,54 @@ "Inline Movie": "Off" }, "Routine": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", + "Thickness F >> H": "36 mm", "VoI A >> P": "400 mm", "VoI R >> L": "400 mm", - "TR": "1500.0 ms", + "TR": "3000.0 ms", "TE": "2.30 ms", - "Averages": "2" + "Averages": "60" }, "Contrast - Common": { - "TR": "1500.0 ms", + "TR": "3000.0 ms", "TE": "2.30 ms", "Flip Angle": "90 deg", - "Preparation Scans": "4", - "Averages": "2", - "Water Suppression": "Water Saturation", - "Water Suppr. BW": "35 Hz" + "Preparation Scans": "8", + "Averages": "60", + "Water Suppression": "None" }, "Resolution - Common": { "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", - "Scan Res. A >> P": "16", - "Scan Res. R >> L": "16", - "Interpol. Res. A >> P": "16", - "Interpol. Res. R >> L": "16", + "Thickness F >> H": "36 mm", + "Scan Res. A >> P": "8", + "Scan Res. R >> L": "8", + "Interpol. Res. A >> P": "8", + "Interpol. Res. R >> L": "8", "Hamming": "Off", "Dimension": "2D", - "Phase Encoding": "Full", + "Phase Encoding": "Weighted", "Vector Size": "512", "Normalize": "Off" }, "Geometry - Common": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", + "Thickness F >> H": "36 mm", "VoI A >> P": "400 mm", "VoI R >> L": "400 mm" }, "Geometry - AutoAlign": { "Slice Group": "1", - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Phase Encoding Dir.": "A >> P", "AutoAlign": "---", "Initial Position": "Isocenter", @@ -1626,49 +1625,58 @@ "Adjust with Body Coil": "Off", "Confirm Frequency": "Never", "Assume Silicone": "Off", - "Adj. Water Suppr.": "On" + "Adj. Water Suppr.": "Off" }, "System - Adjust Volume": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "A >> P": "400 mm", "R >> L": "400 mm", - "F >> H": "25 mm", + "F >> H": "36 mm", "Reset": "Off" }, "System - pTx": { "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 31P": "49.891823 MHz", + "Frequency 1H": "123.249275 MHz", + "? Ref. Amplitude 31P": "0.000 V", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" }, "Physio - Signal": { "1st Signal/Mode": "None", - "TR": "1500.0 ms" + "TR": "3000.0 ms" }, "Sequence - Common": { "Sequence Name": "csi_fid", - "Preparation Scans": "4", + "Preparation Scans": "8", "Delta Frequency": "0.00 ppm", "Measurements": "1", "Dimension": "2D", "Save Uncombined": "Off", "Acquisition Delay": "2.30 ms", - "Bandwidth": "1000 Hz", - "Acquisition Duration": "512 ms", + "Bandwidth": "4000 Hz", + "Acquisition Duration": "128 ms", "Remove Oversampling": "On" }, "Sequence - Nuclei": { - "TX/RX Nucleus": "1H", + "TX/RX Nucleus": "31P", "TX/RX Delta Frequency": "0 Hz", - "NOE Type": "None", - "TX Nucleus": "None", + "NOE Type": "Rectangular", + "NOE Count": "1", + "NOE Duration": "5.00 ms", + "NOE Flip Angle": "90.00 deg", + "TX Nucleus": "1H", "TX Delta Frequency": "0 Hz", - "Decoupling Type": "None" + "Decoupling Type": "Waltz4", + "Decoupling Duration": "1.00 ms", + "DC Total Duration": "50.00 %", + "DC Pause Fract.": "100.00 %", + "Decoupling Flip Angle": "180.00 deg" } }, "pages": [ @@ -1681,9 +1689,9 @@ "name": "head_csi_fid", "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", "header": { - "ta": "12:54 min", + "ta": "14:36 min", "coil_selection": "Auto", - "voxel_size_mm": "25.0×25.0×25.0", + "voxel_size_mm": "50.0×50.0×40.0", "rel_snr": "1.00", "sequence": "csi_fid" }, @@ -1711,55 +1719,54 @@ "Inline Movie": "Off" }, "Routine": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", + "Thickness F >> H": "40 mm", "VoI A >> P": "400 mm", "VoI R >> L": "400 mm", - "TR": "1500.0 ms", + "TR": "3000.0 ms", "TE": "2.30 ms", - "Averages": "2" + "Averages": "22" }, "Contrast - Common": { - "TR": "1500.0 ms", + "TR": "3000.0 ms", "TE": "2.30 ms", "Flip Angle": "90 deg", - "Preparation Scans": "4", - "Averages": "2", - "Water Suppression": "Water Saturation", - "Water Suppr. BW": "35 Hz" + "Preparation Scans": "8", + "Averages": "22", + "Water Suppression": "None" }, "Resolution - Common": { "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", - "Scan Res. A >> P": "16", - "Scan Res. R >> L": "16", - "Interpol. Res. A >> P": "16", - "Interpol. Res. R >> L": "16", - "Hamming": "Off", + "Thickness F >> H": "40 mm", + "Scan Res. A >> P": "8", + "Scan Res. R >> L": "8", + "Interpol. Res. A >> P": "8", + "Interpol. Res. R >> L": "8", + "Hamming": "On", "Dimension": "2D", - "Phase Encoding": "Full", + "Phase Encoding": "Weighted", "Vector Size": "512", "Normalize": "Off" }, "Geometry - Common": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "FOV A >> P": "400 mm", "FOV R >> L": "400 mm", - "Thickness F >> H": "25 mm", + "Thickness F >> H": "40 mm", "VoI A >> P": "400 mm", "VoI R >> L": "400 mm" }, "Geometry - AutoAlign": { "Slice Group": "1", - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Phase Encoding Dir.": "A >> P", "AutoAlign": "---", "Initial Position": "Isocenter", @@ -1785,49 +1792,59 @@ "Adjust with Body Coil": "Off", "Confirm Frequency": "Never", "Assume Silicone": "Off", - "Adj. Water Suppr.": "On" + "Adj. Water Suppr.": "Off" }, "System - Adjust Volume": { - "Position": "Isocenter", - "Orientation": "Transversal", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C-17.0", "Rotation": "0.00 deg", "A >> P": "400 mm", "R >> L": "400 mm", - "F >> H": "25 mm", + "F >> H": "40 mm", "Reset": "Off" }, "System - pTx": { "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 31P": "49.891823 MHz", + "Frequency 1H": "123.249275 MHz", + "? Ref. Amplitude 31P": "0.000 V", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" }, "Physio - Signal": { "1st Signal/Mode": "None", - "TR": "1500.0 ms" + "TR": "3000.0 ms" }, "Sequence - Common": { "Sequence Name": "csi_fid", - "Preparation Scans": "4", + "Preparation Scans": "8", "Delta Frequency": "0.00 ppm", "Measurements": "1", "Dimension": "2D", "Save Uncombined": "Off", "Acquisition Delay": "2.30 ms", - "Bandwidth": "1000 Hz", - "Acquisition Duration": "512 ms", + "Bandwidth": "4000 Hz", + "Acquisition Duration": "128 ms", "Remove Oversampling": "On" }, "Sequence - Nuclei": { - "TX/RX Nucleus": "1H", + "TX/RX Nucleus": "31P", "TX/RX Delta Frequency": "0 Hz", - "NOE Type": "None", - "TX Nucleus": "None", + "NOE Type": "Rectangular", + "NOE Count": "10", + "NOE Duration": "5.00 ms", + "NOE Pause": "10.00 ms", + "NOE Flip Angle": "90.00 deg", + "TX Nucleus": "1H", "TX Delta Frequency": "0 Hz", - "Decoupling Type": "None" + "Decoupling Type": "Waltz4", + "Decoupling Duration": "1.00 ms", + "DC Total Duration": "50.00 %", + "DC Pause Fract.": "100.00 %", + "Decoupling Flip Angle": "180.00 deg" } }, "pages": [ @@ -2004,7 +2021,7 @@ "LR Balancing": "Off" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" @@ -2254,7 +2271,7 @@ "LR Balancing": "Off" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" @@ -2496,7 +2513,7 @@ "B1 Shim": "TrueForm" }, "System - Tx/Rx": { - "Frequency 1H": "123.249491 MHz", + "Frequency 1H": "123.249275 MHz", "? Ref. Amplitude 1H": "0.000 V", "Reset": "Off", "Image Scaling": "1.000" diff --git a/tests/golden/XA60-CHR-MDD.json b/tests/golden/XA60-CHR-MDD.json new file mode 100644 index 0000000..0ea0891 --- /dev/null +++ b/tests/golden/XA60-CHR-MDD.json @@ -0,0 +1,5928 @@ +{ + "source_file": "examples/XA60/CHR-MDD.pdf", + "software_version": "XA60", + "detection": { + "method": "header-string", + "confidence": "high" + }, + "scanner": "SIEMENS MAGNETOM 3.0T XR Numaris/X VA60A-0D4N", + "page_count": 60, + "front_matter_pages": [ + 1 + ], + "scans": [ + { + "index": 0, + "name": "Localizer", + "path": "\\\\Research\\Investigators\\Millman\\CHR-MDD\\Localizer", + "header": { + "ta": "9 sec", + "coil_selection": "Auto", + "voxel_size_mm": "1.2×1.2×5.0", + "pat": "None", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "FLASH -- spoiled gradient echo", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "On", + "Start measurements": "Single Measurement", + "Prio Recon": "On", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "Off", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "On", + "Load Images to Graphic Segments": "On", + "Graphic segment": "All Segments", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "1", + "Distance Factor": "20 %", + "Position": "L0.0 A45.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Slice Group #2": "2", + "Slices #2": "1", + "Distance Factor #2": "20 %", + "Position #2": "L0.0 A45.0 H0.0 mm", + "Orientation #2": "Transversal", + "Phase Encoding Dir. #2": "A >> P", + "Slice Group #3": "3", + "Slices #3": "1", + "Distance Factor #3": "20 %", + "Position #3": "L0.0 A45.0 H0.0 mm", + "Orientation #3": "Transversal", + "Phase Encoding Dir. #3": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "TR": "40.0 ms", + "TE": "3.00 ms", + "Averages": "1", + "Concatenations": "1", + "AutoAlign": "---" + }, + "Contrast - Common": { + "TR": "40.0 ms", + "TE": "3.00 ms", + "MTC": "Off", + "Magn. 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Preparation": "None", + "Flip Angle": "15 deg", + "Fat-Water Contrast": "Standard", + "Dark Blood": "Off", + "Contrasts": "1", + "SWI": "Off", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "1", + "Multiple Series": "Off" + }, + "Resolution - Common": { + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "Base Resolution": "256", + "Phase Resolution": "75 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "None", + "Deep Resolve": "Off", + "Phase Partial Fourier": "Off", + "Asymmetric Echo": "Allowed" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "On", + "Distortion Correction": "2D", + "Normalize": "Prescan", + "Image Filter": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "1", + "Distance Factor": "20 %", + "Position": "L0.0 A45.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Slice Group #2": "2", + "Slices #2": "1", + "Distance Factor #2": "20 %", + "Position #2": "L0.0 A45.0 H0.0 mm", + "Orientation #2": "Transversal", + "Phase Encoding Dir. #2": "A >> P", + "Slice Group #3": "3", + "Slices #3": "1", + "Distance Factor #3": "20 %", + "Position #3": "L0.0 A45.0 H0.0 mm", + "Orientation #3": "Transversal", + "Phase Encoding Dir. #3": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "TR": "40.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "L0.0 A45.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Slice Group #2": "2", + "Position #2": "L0.0 A45.0 H0.0 mm", + "Orientation #2": "Transversal", + "Phase Encoding Dir. #2": "A >> P", + "Slice Group #3": "3", + "Position #3": "L0.0 A45.0 H0.0 mm", + "Orientation #3": "Transversal", + "Phase Encoding Dir. #3": "A >> P", + "AutoAlign": "---", + "Initial Position": "L0.0 A45.0 H0.0", + "L": "0.0 mm", + "A": "45.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Saturation Mode": "Standard", + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "0 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "ACS All but spine", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Sum of Squares", + "Matrix Optimization": "Off", + "Coil Focus": "Flat" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Tune up", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "263 mm", + "R >> L": "350 mm", + "F >> H": "350 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Slice-sel.", + "LR Balancing": "Off" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249275 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "40.0 ms", + "Segments": "1", + "Concatenations": "1" + }, + "Physio - Cardiac": { + "Fat-Water Contrast": "Standard", + "Magn. Preparation": "None", + "Dark Blood": "Off", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Phase Resolution": "75 %" + }, + "Physio - PACE": { + "Resp. Control": "Off", + "Concatenations": "1" + }, + "Inline - Liver": { + "Liver Registration": "Off", + "Save Original Images": "On" + }, + "Inline - Subtraction": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Save Original Images": "On" + }, + "Inline - MIP": { + "MIP Sag": "Off", + "MIP Cor": "Off", + "MIP Tra": "Off", + "MIP Time": "Off", + "Radial MIP": "Off", + "Save Original Images": "On", + "MPR Sag": "Off", + "MPR Cor": "Off", + "MPR Tra": "Off" + }, + "Inline - Soft Tissue": { + "Wash-in": "Off", + "Wash-out": "Off", + "TTP": "Off", + "PEI": "Off", + "MIP Time": "Off", + "Measurements": "1" + }, + "Inline - Composing": { + "Inline Composing": "Off" + }, + "Sequence - Part 1": { + "Sequence Name": "fl", + "Dimension": "2D", + "Excitation": "Slice-sel.", + "RF Pulse Type": "Normal", + "Gradient Mode": "Fast", + "Flow Compensation": "None", + "Bandwidth": "260 Hz/Px", + "Asymmetric Echo": "Allowed", + "Segments": "1" + }, + "Sequence - Part 2": { + "Introduction": "On", + "RF Spoiling": "On", + "Acoustic noise reduction": "Off" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off", + "Allowed Delay": "0 s" + } + }, + "pages": [ + 52, + 53, + 54 + ] + }, + { + "index": 22, + "name": "reward2", + "path": "\\\\Research\\Investigators\\Millman\\ZMK23 with Physio\\reward2", + "header": { + "ta": "13:16 min", + "coil_selection": "Manual", + "voxel_size_mm": "2.0×2.0×2.0", + "pat": "None", + "rel_snr": "1.00", + "sequence": "epfid" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "multiband EPI, BOLD", + "signature": "cmrr-mb-epi-bold", + "evidence": [ + "Special card prints MB LeakBlock kernel, Online multi-band recon." + ], + "special_parameters": 18 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "On", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "On", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "72", + "Distance Factor": "0 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "208 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.0 mm", + "TR": "800.0 ms", + "TE": "37.00 ms", + "Averages": "1", + "Multi-band accel. factor": "8", + "AutoAlign": "Head > Brain", + "Coil Elements": "HC1-7" + }, + "Contrast - Common": { + "TR": "800.0 ms", + "TE": "37.00 ms", + "MTC": "Off", + "Magn. Preparation": "None", + "Flip Angle": "52 deg", + "Fat-Water Contrast": "Fat Saturation", + "Contrasts": "1", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "983", + "Delay in TR": "0.00 ms" + }, + "Resolution - Common": { + "FOV Read": "208 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.0 mm", + "Base Resolution": "104", + "Phase Resolution": "72 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "None", + "Phase Partial Fourier": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Hamming": "Off", + "Distortion Correction": "3D", + "Static Field Correction": "Off", + "Normalize": "Prescan" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "72", + "Distance Factor": "0 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "208 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.0 mm", + "TR": "800.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Multi-band accel. factor": "8" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "0 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "Manual", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Sum of Squares", + "Matrix Optimization": "Off" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Standard", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "On", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "208 mm", + "R >> L": "208 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249275 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Correction Factor": "1.00", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "800.0 ms", + "Log Signals": "Off", + "Multi-band accel. factor": "8" + }, + "BOLD": { + "GLM Statistics": "Off", + "Ignore Meas. at Start": "0", + "Ignore After Transition": "0", + "Model Transition States": "On", + "Temp. Highpass Filter": "On", + "Threshold": "4.00", + "Paradigm Size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion Correction": "Off", + "Spatial Filter": "Off", + "Measurements": "983", + "Delay in TR": "0.00 ms" + }, + "Sequence - Part 1": { + "Sequence Name": "epfid", + "Dimension": "2D", + "Excitation": "Standard", + "Gradient Mode": "Performance", + "Flow Compensation": "None", + "Bandwidth": "2290 Hz/Px", + "Echo Spacing": "0.58 ms", + "Free Echo Spacing": "Off", + "EPI Factor": "75" + }, + "Sequence - Part 2": { + "Introduction": "Off", + "RF Spoiling": "Off" + }, + "Sequence - Special": { + "Excite pulse duration": "6600 us", + "Min. prep scans": "0", + "Min. prep scans SB": "0", + "Delay before PC scans": "0 us", + "Single-band images": "On", + "MB LeakBlock kernel": "On", + "MB dual kernel": "Off", + "MB RF phase scramble": "On", + "Opt. MB RF pulse BW": "Off", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "Off", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "On", + "Force equal slice timing": "Off", + "Online multi-band recon.": "Online", + "FFT scale factor": "1.00", + "Physio recording": "DICOM", + "Triggering scheme": "Standard" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off" + } + }, + "pages": [ + 55, + 56 + ] + } + ] +} diff --git a/tests/test_exar.py b/tests/test_exar.py index b83860e..8d0f3ad 100644 --- a/tests/test_exar.py +++ b/tests/test_exar.py @@ -301,8 +301,19 @@ def test_step_order_is_the_link_chain_not_the_children_blob(protocol_archive_pat @requires_exar -def test_every_step_is_named_and_holds_a_protocol(protocol_archive_path: str) -> None: - """Names resolve through the label element, and each step runs a protocol. +def test_every_step_is_named_and_measurement_steps_hold_a_protocol( + protocol_archive_path: str, +) -> None: + """Names resolve, and a step holds a protocol exactly when it acquires one. + + The running order mixes two kinds. An ``EdfMeasurementStep`` runs a + protocol; an ``EdfPauseStep`` is an instruction an operator put between + scans -- "Count down with RA to start of scan" -- and holds none. Both are + named and both are in the chain, so walking scans means skipping the + second rather than assuming it cannot happen. + + The two signals are checked against each other: the instance kind and the + presence of a protocol must agree, since either alone could be wrong. Parameters ---------- @@ -317,7 +328,31 @@ def test_every_step_is_named_and_holds_a_protocol(protocol_archive_path: str) -> assert steps for step in steps: assert step.name, f"step {step.instance.object_id} has no name" - assert step.protocol.xprotocol.startswith("") + assert step.is_pause != step.runs_a_protocol, ( + f"{step.name}: kind is {step.instance.kind} but " + f"{'no ' if not step.runs_a_protocol else ''}protocol is attached" + ) + if step.runs_a_protocol: + assert step.protocol.xprotocol.startswith("") + + +@requires_exar +def test_a_pause_step_is_a_real_thing_the_corpus_contains() -> None: + """At least one archive exercises the protocol-less step. + + A branch nothing reaches is a claim about the code rather than the format, + and this one was written only because three archives arrived carrying + eleven pause steps each and the reader raised on all of them. + + Returns + ------- + None + """ + archive = exar.read(find_exar("CHR-MDD.exar1")) + pauses = [step for step in archive.steps if step.is_pause] + assert pauses, "no pause step in this archive, so the handling is untested" + assert all(not step.protocols for step in pauses) + assert all(step.name for step in pauses) @requires_exar @@ -337,6 +372,8 @@ def test_protocol_previews_carry_the_labels_the_pdf_prints(archive_path: str) -> None """ for step in exar.read(archive_path).steps: + if not step.runs_a_protocol: + continue entries = step.protocol.preview assert entries assert "$id" not in entries @@ -360,6 +397,8 @@ def test_a_protocol_still_carries_an_ascconv_block(archive_path: str) -> None: None """ for step in exar.read(archive_path).steps: + if not step.runs_a_protocol: + continue text = step.protocol.xprotocol assert "### ASCCONV BEGIN" in text assert "### ASCCONV END" in text @@ -428,8 +467,8 @@ def test_a_written_archive_reads_back_to_the_same_tree( assert written.baseline == original.baseline assert written.head == original.head assert [s.name for s in written.steps] == [s.name for s in original.steps] - assert [s.protocol.xprotocol for s in written.steps] == [ - s.protocol.xprotocol for s in original.steps + assert [s.protocol.xprotocol for s in written.steps if s.runs_a_protocol] == [ + s.protocol.xprotocol for s in original.steps if s.runs_a_protocol ] diff --git a/tests/test_exar_patch.py b/tests/test_exar_patch.py index 4ab5ec2..a1db9c3 100644 --- a/tests/test_exar_patch.py +++ b/tests/test_exar_patch.py @@ -705,6 +705,8 @@ def test_every_shipped_mapping_agrees_with_the_corpus(protocol_archive_path: str archive = read(protocol_archive_path) checked = 0 for step in archive.steps: + if not step.runs_a_protocol: + continue protocol = step.protocol for mapping in patch.MAPPINGS: if mapping.preview_path is None or not patch.applies_to(mapping, protocol): @@ -856,6 +858,8 @@ def test_the_sequence_build_stamp_is_stable_where_the_guid_beside_it_is_not() -> archive = read(find_exar("CMRR_optionscan_P1.exar1")) stamps, guids = set(), set() for step in archive.steps: + if not step.runs_a_protocol: + continue if not patch.sequence_of(step.protocol).startswith("cmrr_"): continue raw = patch.read_ascconv(step.protocol.xprotocol, "sWipMemBlock.tFree") @@ -1000,6 +1004,8 @@ def test_no_protocol_has_two_mappings_writing_one_key(protocol_archive_path: str """ archive = read(protocol_archive_path) for step in archive.steps: + if not step.runs_a_protocol: + continue protocol = step.protocol keys = [(m.ascconv_key, m.bit) for m in patch.MAPPINGS if patch.applies_to(m, protocol)] assert len(keys) == len(set(keys)), ( diff --git a/tests/test_scans.py b/tests/test_scans.py index 5f20cc2..095bdde 100644 --- a/tests/test_scans.py +++ b/tests/test_scans.py @@ -79,6 +79,14 @@ "XA60/NAV_optionscan_P1.pdf": 31, "VE11C/31P CSI 20230503 NOE.pdf": 13, "XA60/31P CSI 20230503 NOE.pdf": 13, + # Both counts confirmed against their own contents pages. Note that these + # two PDFs do NOT match the .exar1 shipped beside them: CHR-MDD's archive + # holds 23 acquisitions against the printout's 24, and the 31P archive + # holds 24 against its printout's 13. The pairs are different versions of + # their protocols, which is a fact about the corpus rather than a parse + # error -- ZMK23's pair does agree, at 23 each. + "XA60/CHR-MDD.pdf": 24, + "XA60/ZMK23 with Physio.pdf": 23, "VE11C/BEEST_SPICE_11112025.pdf": 24, "Potpourri_P1.pdf": 18, "Potpourri_P1_changed.pdf": 18,